Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • GenoMax
    replied
    Can you try removing the two track definition lines at the top and see if that works?

    Leave a comment:


  • munnj90
    replied
    I re-build/renamed the reference genomes so that bowtie can find the files. Is this potentially and issue caused by my .gff file? - as far as i'm aware it should be fine (they ask for .gtf). I've put the top 20 lines below.


    -------------------
    ##gff-version 2
    # seqname source feature start end score strand frame attributes
    pSVEN - source 1 158122 . + . mol_type "genomic DNA" ; strain "ATCC 10712" ; organism "Streptomyces venezuelae"
    pSVEN - CDS 481 717 . + . locus_tag "pSVEN15_0001" ; inference "ab initio prediction:Prodigal:2.6" ; codon_start 1 ; translation "MRSIFGAMRSRIPRCAGTIRAAVKAVYDGLFWPRRDGFVWPRLRNGLKWPHLVALSMSTDSEYSPLREAPGIRTARDL" ; product "hypothetical protein" ; transl_table 11
    pSVEN - sig_peptide 481 546 . + . locus_tag "pSVEN15_00001" ; inference "ab initio prediction:SignalP:4.1" ; note "predicted cleavage at residue 22"
    pSVEN - CDS 736 1278 . - . locus_tag "pSVEN15_0002" ; inference "ab initio prediction:Prodigal:2.6" ; codon_start 1 ; translation "MTDTRDQRPAEATLDFLRSAFPPEWREPALGHEAVADWEQENGVALPEPYRTFIAEISNGSSLGPADDGGLQPLGWLPDSWPDLGPRQPGEPFPLEAAWPWEDDESVDPEDPRIDAAFTKGSIVLGSEDGQSFWLLLTAGPRRGEVWMIADVGAVPAPGDQAWGFEEWVQRWHTGNDWWN" ; product "hypothetical protein" ; transl_table 11
    pSVEN - CDS 1496 1906 . + . locus_tag "pSVEN15_0003" ; inference "ab initio prediction:Prodigal:2.6" ; codon_start 1 ; translation "MTYRFTARAATTEIDPDGYFTEAALAEGEDGSGFILMFMAGEEEPDAQDVELGMDTHCLVTAGQGTAYGCVREAVLDGNVLRISLDPEALESLRLDEGEIEAVIEAPTEDVARFREVLAQVLTYGRADAVPTRLAV" ; product "hypothetical protein" ; transl_table 11
    pSVEN - CDS 2099 2536 . - . locus_tag "pSVEN15_0004" ; inference "ab initio prediction:Prodigal:2.6" ; codon_start 1 ; translation "MTADWYVLIEEDTRTTERADGTELKLHRWMLTGTHRIGPNQAEALEAAEDAALNHLPGILARHARPGEQPARHALLTQDGVWIVLVKQRHRECHIRVTTAQLVHAREEKEAPPKSLKEKLRSAMDGPAPAPKPWSWTPEGKADRT" ; product "hypothetical protein" ; transl_table 11
    pSVEN - CDS 2628 2843 . - . locus_tag "pSVEN15_0005" ; inference "ab initio prediction:Prodigal:2.6" ; codon_start 1 ; translation "MISAMIRPVAGLPTWNHLASSLVLTVLVWAVWYGMQPVYSPCVYFGNHSYEKAVEYGQCDPPKTRVSTWVQ" ; product "hypothetical protein" ; transl_table 11
    pSVEN - CDS 2999 5524 . + . locus_tag "pSVEN15_0006" ; inference "ab initio prediction:Prodigal:2.6" ; inference "protein motif:Pfam:PF03457.8" ; codon_start 1 ; translation "MTAAACALESFATGRILVTVPTLDLLVQTAQAWRAVGHRAPMIAVCSLENDPVLNSLGVRTTTNPVQLALWAGHGPVVVFATYASLVDREDVDAPEGQRKVRGPLEAALTGGERLYGQRMAPFDLAIVDEAHGTAGDLGRPWAAIHDNARIPADFRLYLTATPRILAAPRPQKGADGQEVELATMTDDPNGTYGAWLAELGLSEAIEREILAGFEIDVLEIRDPSPVLGESEEARRGRRLALLQTALLEHAAAWNLRTVMTFHQKVEEAAAFAEKLPETAAELYMNDASDEDLAQAEKLPPSSIDAEFYELDAGRHVPPDRVWSAWLCGDHLVAERREVLRQFANGIDATGRRVHRAFLASCRVLGEGVDITGERGVEAVCFADTRGSQVEIVQNIGRALRLNRDGSTKVARIIVPVFLEPGEDPEDMVASASFKPLVTVLQGLRSHDERMVEQLASRALTSGKRKAHLRRDEDGRIVGAGGAGDGEDQEEGDDTQAAAEAALLHFSSPRNAATIAAFLRTRVYRPESLVWLEGYQALIRWRKENEITGVHAVPYDVEVEVGITKDFPLGRWVHQQRKALRAGELEDRRKRLLDAPEAGMVWEPGEEAWENKLATLRSYRRATGHLAPRQDAVWGEGEAMVPIGQHMANLRRKGGLGKDPKRAAERAAQLAEIDEDWNCPWPLDWQRHYRVLADLVDADGVLPAIEPGVLFEGDDIGRWLERQKNPGTWAQLSTEQQQRLSKLGVQPDQAPSPAPAAAHATKGPSKAQQAFQRGLVALTQWVEREGDRSVPRGHSEQITVDGEAEPVPVKLGVWLSNTKSRRDKLTTEQRAALAALGMKWA" ; product "Helicase associated domain protein" ; transl_table 11
    pSVEN - CDS 5773 6675 . + . locus_tag "pSVEN15_0007" ; inference "ab initio prediction:Prodigal:2.6" ; codon_start 1 ; translation "MFKAAEGVGPQTRPLLVFYGLSQAGRAIAAAAVDLKGEDWNLISHGIHASGYHLDFADIEIRTDPAGTAGSFVRLSELLRSPVWGNDTVVRLEEVWDTLPANLQYPLTGRERFTPLYASADSIDGTDFHPLLTLHVGDILDRVVDDGSRTALDEFLQSYPGTAGYEEFARRRMGAGAEPDYVRHHPNAGWLYMHWKMAAETGTKEERLERLSTMTRSYAGHRYFFPAVAGLPRELHPLMAWWAVLYALSMLARYQPAQWANHINVDGSRHAVPIEKILERAMEHLPVLIADTIEEVAAWP" ; product "hypothetical protein" ; transl_table 11
    pSVEN - CDS 6792 7727 . + . locus_tag "pSVEN15_0008" ; inference "ab initio prediction:Prodigal:2.6" ; codon_start 1 ; translation "MLFEQRMYAHVKFLELMAELYENEFEDFFHRLMCLRYPDFLDVRTAGSLGDRSADGLSLHSRKLYACYAPQTVKPDKIRKKFEGDLSGAVTKRNGEFDTFVFVHNDRRGVHPEVTSLLASARDSMPSLRFEQMGTRRLWRECMQLDQMETEDVLRCEIPIKETTFGIGMEDLAPLLKQLQDIRAESNPLMSLPDVSVEKLDFNQIEGADREDLLRGMRQSYLVDAFYAGTRSELEHDEVAEGFRLYYQQVRRDYSDADDVLWQLKMYFLGSAQPRPKVLRAALVVLAHFFERCDIFETPPAGWQPGIGLTA" ; product "hypothetical protein" ; transl_table 11
    pSVEN - CDS 7724 7990 . + . locus_tag "pSVEN15_0009" ; inference "ab initio prediction:Prodigal:2.6" ; codon_start 1 ; translation "MITPTKGIAPDRCLLAVGAQVLLQLDEPRTVSQTWARLKSWRADQAHTSPVSFEWFVLALDILFAMGAVELVQDVLVARSTDAAPSER" ; product "hypothetical protein" ; transl_table 11
    pSVEN - CDS 7968 9728 . + . locus_tag "pSVEN15_0010" ; inference "ab initio prediction:Prodigal:2.6" ; codon_start 1 ; translation "MLRRLSADDARFKTVEFSPGLNLLVADTTSSSAETDSRNSAGKSSVIELIHFLLGAKSAGSLATNKALRHITFSLAMDWPWQDAPVEVRRRGDNPKVVRLSQDVSGVPADTLFTDSQDVELSVEQWNRVIERDLFGLEGDHPGVSGRTLLSFLIRRVSAHGFNEPTRTFSRQAAAEASSNLAYLLGLDWQLVNGYRELNARKATRDQLRKAVNDPVWGRIVGSTADLRGQITLAEAQVERLRAQVAAFQVVPEYERLKERADQVSRRIKQLAQEDVIDQHNLEELQSAVTETTDVEVSYLEPAYRELGVILNDQVRRRFDDVKAFHHSVVRNRRRFLEEEIQELTARLAARRQERADLGEDQARLLRELADGGALEALTALQTALGREEAALGALRHRFDAAQALEASARQITAKSVELQQAVDLDLQERRQQTDEAILLFSRYAQRLYGEGREAYLAIEAGRTSLSITPRIDADDSRGINNMVIFCFDLTLAVLAHRHERGPDFLIHDSHLYDGVDERQVARALALAAEVTEEEHMQYIVTLNTDTLSTAAQRGFDPEPHIRSPRLTDDEEGGLFGFRFKAAGKA" ; product "hypothetical protein" ; transl_table 11
    pSVEN - CDS 9883 10203 . - . locus_tag "pSVEN15_0011" ; inference "ab initio prediction:Prodigal:2.6" ; codon_start 1 ; translation "MHSLRFTEDADETLNRLTVGSKADPAKLKKVNNALARLQANPRHPGLHSHQYENFPGHASEKVWDSYVENHNPSAWRIYWMYGPDERNAAGETISVITVLVIGPHP" ; product "hypothetical protein" ; transl_table 11
    pSVEN - CDS 10210 10512 . - . locus_tag "pSVEN15_0012" ; inference "ab initio prediction:Prodigal:2.6" ; codon_start 1 ; translation "MTAIHEREEFEIVAETEVDSRGRVSLGRAGARPGRRYRVESNPDGVLLLTPVVSIPEREMQVWNDPHLAERIRTGIEQAKAGKTIDRGDFSHYLDEDDED" ; product "hypothetical protein" ; transl_table 11
    pSVEN - CDS 10654 11499 . - . locus_tag "pSVEN15_0013" ; inference "ab initio prediction:Prodigal:2.6" ; codon_start 1 ; translation "MFCGVKQQTSQKPVASSAQTREALLERAARDFAPIRRAFVQKKRDEADRSSRLAEFVTNGDVRGLRAYLFIVAITSAETAESGWSTTLPGMVWARAFGTTEDATPASARTAVTKVLKRLEERRLITYERPKGTWDIQVTLLREDGSLDPYTRPGNQNRDAYLKIPFELWRTGLIDQLGLPALAMLLTASCEPAFFELPTERMKEWYGWSPDTAERGFRQLAKEGVLQVHKTYIAAPLSPTGTAEVNRYVLLPPFIARSARKKAPSMENTVETTGDAQALGH" ; product "hypothetical protein" ; transl_table 11
    pSVEN - CDS 12187 12744 . + . locus_tag "pSVEN15_0014" ; inference "ab initio prediction:Prodigal:2.6" ; codon_start 1 ; translation "MGQIEEGLERALRTRPVPSSTGARLRFLLAAHRGSTRQVAAVLGVSQRTVQRWVTEKPGARRPPGPTQVRAIEEAVLARWQPRVRARRRAQAEAEGFVFHTRARFGFAAAAGSSDDPRVRWITQDLPGEVARELFAARDAGAGEQQQTVILARALGHAYFREWGRRAHGLHIAFGDIEFADFSIG" ; product "hypothetical protein" ; transl_table 11
    pSVEN - CDS 12777 13856 . - . locus_tag "pSVEN15_0015" ; inference "ab initio prediction:Prodigal:2.6" ; codon_start 1 ; translation "MVIDRHDDVIHTRTALAAHHLPSGRITLHPGPGTTSDTGLAHDLLAALGKPPLLTGRFPAGRQPAWEAAAAWMTALPVTRLTVLRAHRLTTRRTMRLLELRALTGIHLTLVCHRPHLPAALHQALQTADYSLTTDLDAACRHYYGTPVTEPPLADEPAGPTGRWLTLPALERLISYDSPRPCTDPCTPPPITWRHRPPPVPLTAHTAQRVAQRLHAATAHPRLAAAIASALFTGTSLQQLATARPRDYDTAAATLALHDRARYTDGCAAHPVPPWASVFLQAAACFTRLVSGEDQELLAAPGDRVHLLCVAETAKLRPPQPPAACRKAPVGRVEWDWRERQEAERYEAVPTSRVRPSRR" ; product "hypothetical protein" ; transl_table 11
    pSVEN - CDS 13903 14646 . - . locus_tag "pSVEN15_0016" ; inference "ab initio prediction:Prodigal:2.6" ; codon_start 1 ; translation "MTAATYQYVDLPDASVVTTRALLTARENITDTVAARAMMCIHGGAGFGKTLAVNTCLRALEPGEDVRKITFRARPTARAVRYELFTALDLAGEPPRHPSEFDRLLKTALAERPRTFLVDEAQWLNGEAFEYFRYLWDEPSTQLAIIFVGGEGCHTVLRREPMLSSRIFIWQHFTRLTPSEVLDVIPLFHPIWADAAPEDIAFADQHAAHGNFRAWAQLTAHTRTALARTGRPRVDQELLRWAFSRLA" ; product "hypothetical protein" ; transl_table 11

    ------------------------

    Leave a comment:


  • munnj90
    replied
    Yes, it is a single fasta sequence containing file.

    Leave a comment:


  • GenoMax
    replied
    Does pSVEN.fa contain only the plasmid? It does not have more than one fasta sequence in it, correct?

    Leave a comment:


  • munnj90
    replied
    This is a small plasmid found within our strain so i would expect a low relative alignement.

    Here are the alignment summaries:

    5_psven15 (wt):
    Reads:
    Input : 5975994
    Mapped : 28670 ( 0.5% of input)
    of these: 24 ( 0.1%) have multiple alignments (0 have >20)
    0.5% overall read mapping rate.

    7_psven15 (RsrR):
    Reads:
    Input : 15786210
    Mapped : 104959 ( 0.7% of input)
    of these: 93 ( 0.1%) have multiple alignments (0 have >20)
    0.7% overall read mapping rate.

    Using your suggested command i get the same error message. I also tried it on the whole genome sample to get the same result.

    Here is the tophat report WT then mutant:

    [2016-03-01 15:20:45] Beginning TopHat run (v2.0.14)
    -----------------------------------------------
    [2016-03-01 15:20:45] Checking for Bowtie
    Bowtie version: 2.2.2.0
    [2016-03-01 15:20:45] Checking for Bowtie index files (genome)..
    [2016-03-01 15:20:45] Checking for reference FASTA file
    Warning: Could not find FASTA file /gpfs/home/ezx11reu/John/ChIP-seq/reference_genome/indexed_genomes/tophat/pSVEN.fa.fa
    [2016-03-01 15:20:45] Reconstituting reference FASTA file from Bowtie index
    Executing: /gpfs/grace/bowtie2-2.2.2/bowtie2-inspect /gpfs/home/ezx11reu/John/ChIP-seq/reference_genome/indexed_genomes/tophat/pSVEN.fa > /gpfs/home/ezx11reu/John/tophat_rna-seq/psven15/5_psven15/tmp/pSVEN.fa.fa
    [2016-03-01 15:20:45] Generating SAM header for /gpfs/home/ezx11reu/John/ChIP-seq/reference_genome/indexed_genomes/tophat/pSVEN.fa
    [2016-03-01 15:20:45] Reading known junctions from GTF file
    [2016-03-01 15:20:45] Preparing reads
    left reads: min. length=30, max. length=75, 5975269 kept reads (725 discarded)
    [2016-03-01 15:23:05] Building transcriptome data files /gpfs/home/ezx11reu/John/tophat_rna-seq/psven15/5_psven15/tmp/pSVEN
    [2016-03-01 15:23:05] Building Bowtie index from pSVEN.fa
    [2016-03-01 15:23:05] Mapping left_kept_reads to transcriptome pSVEN with Bowtie2
    [2016-03-01 15:25:13] Resuming TopHat pipeline with unmapped reads
    [2016-03-01 15:25:13] Mapping left_kept_reads.m2g_um to genome pSVEN.fa with Bowtie2
    [2016-03-01 15:32:07] Mapping left_kept_reads.m2g_um_seg1 to genome pSVEN.fa with Bowtie2 (1/3)
    [2016-03-01 15:33:20] Mapping left_kept_reads.m2g_um_seg2 to genome pSVEN.fa with Bowtie2 (2/3)
    [2016-03-01 15:34:26] Mapping left_kept_reads.m2g_um_seg3 to genome pSVEN.fa with Bowtie2 (3/3)
    [2016-03-01 15:35:00] Retrieving sequences for splices
    [2016-03-01 15:35:00] Indexing splices
    Building a SMALL index
    [2016-03-01 15:35:01] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
    [2016-03-01 15:35:32] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
    [2016-03-01 15:36:04] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
    [2016-03-01 15:36:20] Joining segment hits
    [2016-03-01 15:36:39] Reporting output tracks
    -----------------------------------------------
    [2016-03-01 15:38:53] A summary of the alignment counts can be found in /gpfs/home/ezx11reu/John/tophat_rna-seq/psven15/5_psven15/align_summary.txt
    [2016-03-01 15:38:53] Run complete: 00:18:08 elapsed





    [2016-03-01 15:43:35] Beginning TopHat run (v2.0.14)
    -----------------------------------------------
    [2016-03-01 15:43:35] Checking for Bowtie
    Bowtie version: 2.2.2.0
    [2016-03-01 15:43:36] Checking for Bowtie index files (genome)..
    [2016-03-01 15:43:36] Checking for reference FASTA file
    Warning: Could not find FASTA file /gpfs/home/ezx11reu/John/ChIP-seq/reference_genome/indexed_genomes/tophat/pSVEN.fa.fa
    [2016-03-01 15:43:36] Reconstituting reference FASTA file from Bowtie index
    Executing: /gpfs/grace/bowtie2-2.2.2/bowtie2-inspect /gpfs/home/ezx11reu/John/ChIP-seq/reference_genome/indexed_genomes/tophat/pSVEN.fa > /gpfs/home/ezx11reu/John/tophat_rna-seq/psven15/7_psven15/tmp/pSVEN.fa.fa
    [2016-03-01 15:43:36] Generating SAM header for /gpfs/home/ezx11reu/John/ChIP-seq/reference_genome/indexed_genomes/tophat/pSVEN.fa
    [2016-03-01 15:43:36] Reading known junctions from GTF file
    [2016-03-01 15:43:36] Preparing reads
    left reads: min. length=30, max. length=75, 15785117 kept reads (1093 discarded)
    [2016-03-01 15:49:46] Building transcriptome data files /gpfs/home/ezx11reu/John/tophat_rna-seq/psven15/7_psven15/tmp/pSVEN
    [2016-03-01 15:49:46] Building Bowtie index from pSVEN.fa
    [2016-03-01 15:49:47] Mapping left_kept_reads to transcriptome pSVEN with Bowtie2
    [2016-03-01 15:56:43] Resuming TopHat pipeline with unmapped reads
    [2016-03-01 15:56:43] Mapping left_kept_reads.m2g_um to genome pSVEN.fa with Bowtie2
    [2016-03-01 16:17:24] Mapping left_kept_reads.m2g_um_seg1 to genome pSVEN.fa with Bowtie2 (1/3)
    [2016-03-01 16:29:26] Mapping left_kept_reads.m2g_um_seg2 to genome pSVEN.fa with Bowtie2 (2/3)
    [2016-03-01 16:31:48] Mapping left_kept_reads.m2g_um_seg3 to genome pSVEN.fa with Bowtie2 (3/3)
    [2016-03-01 16:33:10] Retrieving sequences for splices
    [2016-03-01 16:33:10] Indexing splices
    Building a SMALL index
    [2016-03-01 16:33:10] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
    [2016-03-01 16:33:50] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
    [2016-03-01 16:34:27] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
    [2016-03-01 16:34:48] Joining segment hits
    [2016-03-01 16:35:36] Reporting output tracks
    -----------------------------------------------
    [2016-03-01 16:41:36] A summary of the alignment counts can be found in /gpfs/home/ezx11reu/John/tophat_rna-seq/psven15/7_psven15/align_summary.txt
    [2016-03-01 16:41:36] Run complete: 00:58:00 elapsed

    Leave a comment:


  • GenoMax
    replied
    Can you try

    Code:
    $ cuffdiff -o diff_out6 -b ~/John/ChIP-seq/reference_genome/indexed_genomes/tophat/pSVEN.fa -L WT,MUT ~/John/tophat_rna-seq/psven15/5_psven15/accepted_hits.bam ~/John/tophat_rna-seq/psven15/7_psven15/accepted_hits.bam
    Is this a small dataset or you did not get good alignments? How many sequences did you start with? Can you post the summary of tophat run stats?

    Leave a comment:


  • munnj90
    replied
    Thanks for your response GenoMax.

    I'm only comparing 1 replicate. Below are the respective $ls -lh:

    $ ls -lh ~/John/tophat_rna-seq/psven15/5_psven15/accepted_hits.bam
    $ ls -lh ~/John/tophat_rna-seq/psven15/7_psven15/accepted_hits.bam

    -rw-r--r-- 1 ezx11reu bio 1.5M Mar 8 15:15 /gpfs/home/ezx11reu/John/tophat_rna-seq/psven15/5_psven15/accepted_hits.bam
    -rw-r--r-- 1 ezx11reu bio 4.8M Mar 8 15:59 /gpfs/home/ezx11reu/John/tophat_rna-seq/psven15/7_psven15/accepted_hits.bam

    I just re-ran the files through tophat to make sure they were not interrupted during the processing.

    I just tried a few iterations, removing -L, -u and -p also this:

    cuffdiff -o diff_out6 -b ~/John/ChIP-seq/reference_genome/indexed_genomes/tophat/pSVEN.fa ~/John/tophat_rna-seq/psven15/5_psven15/accepted_hits.bam ~/John/tophat_rna-seq/psven15/7_psven15/accepted_hits.bam

    Which gives me the same error about requiring 2 sam files.

    Leave a comment:


  • GenoMax
    replied
    Are you comparing only one replicate in this case (one WT and one RsrR) files? Are those two file names separated by a space? Have you tried running the program without the -u option (which is for multi-read correction)? Can you show us output of

    Code:
    $ ls -lh ~/John/tophat_rna-seq/psven15/5_psven15/accepted_hits.bam
    $ ls -lh ~/John/tophat_rna-seq/psven15/7_psven15/accepted_hits.bam

    Leave a comment:


  • munnj90
    started a topic error: cuffdiff requires at least 2 sam files

    error: cuffdiff requires at least 2 sam files

    Hi all,

    Sorry I'm aware this has been covered but I've tried the various responses already posted and none of which, unfortunately, have worked. I'm struggling to get the cuffdiff commands to work.

    I've aligned my sequence file (bacterial RNA-seq genome) using tophat:

    tophat -p 8 -G ~/John/ChIP-seq/reference_genome/indexed_genomes/tophat/pSVEN.gff -o ~/John/tophat_rna-seq/psven15/1_psven15 --no-novel-juncs ~/John/ChIP-seq/reference_genome/indexed_genomes/tophat/pSVEN.fa ~/John/RNA-seq/unmodified_seq_files/Sven-WT-8h-minus5PP_S6_R1_001_trimmed.fastq

    This appears to have worked fine.

    I'm carrying out cuffdiff as described in the protocal, here is my commandline:

    cuffdiff -o diff_out6 -b ~/John/ChIP-seq/reference_genome/indexed_genomes/tophat/pSVEN.fa -p 8 -u ~/John/ChIP-seq/reference_genome/indexed_genomes/tophat/pSVEN.gff -L WT,RsrR\
    ~/John/tophat_rna-seq/psven15/5_psven15/accepted_hits.bam ~/John/tophat_rna-seq/psven15/7_psven15/accepted_hits.bam

    I get the error:

    You are using Cufflinks v2.2.1, which is the most recent release.
    Error: cuffdiff requires at least 2 SAM files

    I've tried several iterations of this, minus labels (-L), i orginally had white space character (as is in the paper) behind the "". I've tried with "~/John/..." "./John/..." and "/John/..." for paths.

    All paths can be identified with "ls" and .bam files can be converted to .sam files by "samtools view -h".

    Any help would be greatly appreciated!

Latest Articles

Collapse

  • seqadmin
    Exploring the Dynamics of the Tumor Microenvironment
    by seqadmin




    The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
    07-08-2024, 03:19 PM
  • seqadmin
    Exploring Human Diversity Through Large-Scale Omics
    by seqadmin


    In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
    06-25-2024, 06:43 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 07-10-2024, 07:30 AM
0 responses
30 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-03-2024, 09:45 AM
0 responses
201 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-03-2024, 08:54 AM
0 responses
212 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-02-2024, 03:00 PM
0 responses
194 views
0 likes
Last Post seqadmin  
Working...
X