I need to run Hisat2 on 36 paired-end files. The files are labelled like:
file1_1.fq
file1_2.fq
file2_1.fq
file2_2.fq
...
29 results in 0.0022 seconds.
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Parallelising Hisat2
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BBMAP paired-end alignment problem
Hi All
I'm having a problem with aligning Illumina PE reads with BBMap version 35.92.
Execution of
...Code:bbmap.sh
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BBMAP paired-end alignment problem
Hi All
Trying to use bbmap to align some Illumina PE reads. My command line looks like this
...Code:bbmap.sh overwrite=t ref=A.fasta
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RNA-seq read alignment best practices for low-input Smart-seq2 samples
RNA-seq read alignment best practices for low-input Smart-seq2 samples
Hi All,
I think my data may fall in a nether region between... -
Align full length contigs instead of reads
Hello,
Splice aligners like HiSAT2 and STAR are optimised to map short reads (~100bp) to large genomes. I have assembled contigs available.... -
Mauve exited with error code 11
Greetings,
First of all, I would like to congratulate Koadman and all the team for have developed such an amazing tool as Mauve.
... -
nonunique read mapping and snp calling
Hi all,
We are having a little debate here that we would like some other insights into.
The problem is that we are doing targeted... -
Picard, Markduplicates
We use Picard/CleanSama.jar:
java -Xmx4g -jar $Picard_jarFolder/CleanSam.jar INPUT=$sample OUTPUT=$clean_picard VALIDATION_STRINGENCY=LENIENT... -
Bowtie2 - Concordantly tags.
HI All.
BOWTIE2 OUTPUT:
I have a set of 35 paired sequences.
25 (71.43%) aligned concordantly 0 times.
1 (2.86%) aligned... -
Nextera Expanded Exome BWA aln
Hello,
I'm trying to align Nextera Expanded Exome (62Mb) samples from HiSeq 2000 (Paired end ~99bp insert size) with BWA aln.
... -
What is the diff between sequence align and assembly?
Newbie question.
As I played some bioinfo softwares, sometimes just get confused by the two words, do they mean the same thing?
... -
Any align/assemble tool on reads coverage recommended?
Any good tool recommended to do the align/assemble, since some exons might not be covered in reads. Is there any convenient way or tool to report this?... -
perplexing bowtie2 repeat alignments
I am seeing something perplexing, can you help? I am trying to call variants in plasmids. To do this I am using bowtie2, freebayes and an assortment...Last edited by Mark; 07-12-2013, 07:40 AM. -
Align to fasta
Hi,
i have a question that might be silly...
I need to find in a sequence in fasta format the coordinates corresponding to the reference... -
Align sRNA reads from two libraries
Hi All,
I need to check if there are some common reads between two sRNA libraries. In fact what I trying to do is find specified set miRNAs...
