Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • bioBob
    replied
    Thanks.

    Unfortunately, it appears as though it was a case of RTFM more carefully. Paired reads have to be in fast-a format if in a single file. I only wasted 2 days because I didn't see that earlier. =/

    Leave a comment:


  • jvhaarst
    replied
    It has been a while since I looked at SOAPdenovo, but could you try this config ?
    ----
    #maximal read length
    max_rd_len=100
    [LIB]
    #average insert size
    avg_ins=200
    #if sequence needs to be reversed
    reverse_seq=0
    #in which part(s) the reads are used
    asm_flags=1
    #in which order the reads are used while scaffolding
    rank=1
    q=/common/groups/Illx/Unpaired_SIPES_PF_lane5_1_trimmed.fastq
    q1=/common/groups/Illx/Unpaired_SIPES_PF_lane7_1_trimmed.fastq

    [LIB]
    #average insert size
    avg_ins=200
    #if sequence needs to be reversed
    reverse_seq=0
    #in which part(s) the reads are used
    asm_flags=3
    #in which order the reads are used while scaffolding
    rank=2
    q=/common/groups/Illx/Genomic_SIPES_lane5_1_paired_trimmed_paired.fastq
    q1=/common/groups/Illx/Genomic_SIPES_lane6_1_paired_trimmed_paired.fastq
    q2=/common/groups/Illx/Genomic_SIPES_lane7_1_paired_trimmed_paired.fastq

    Leave a comment:


  • bioBob
    started a topic issues with SOAPdenovo

    issues with SOAPdenovo

    Hello.
    I am wondering if anyone here some some experience with SOAPdenovo.

    I am trying to assembly Illumina data, I have 3 lanes of 101 cycle PE data and 2 lanes of single read data.

    I have tried all sorts of options for running the program down to the default ./SOAPdenovo63mer all -s SOAPdenovo_config.txt -o out_

    At the end of the day (ok, only 2 hours), it is telling me 'no paired reads found' and tossed a terminal error.

    I have used this same data in both CLC and Velvet and it works fine including scaffolding in Velvet and paired mapping in CLC.

    I am sure I am doing something silly. Any thoughts?

    Thanks,
    Bob

    ps. my config file is:

    #maximal read length
    max_rd_len=100
    [LIB]
    #average insert size
    avg_ins=200
    #if sequence needs to be reversed
    reverse_seq=0
    #in which part(s) the reads are used
    asm_flags=1
    #in which order the reads are used while scaffolding
    rank=1
    p=/common/groups/Illx/Genomic_SIPES_lane5_1_paired_trimmed_paired.fastq
    p=/common/groups/Illx/Genomic_SIPES_lane6_1_paired_trimmed_paired.fastq
    p=/common/groups/Illx/Genomic_SIPES_lane7_1_paired_trimmed_paired.fastq
    q=/common/groups/Illx/Unpaired_SIPES_PF_lane5_1_trimmed.fastq
    q=/common/groups/Illx/Unpaired_SIPES_PF_lane7_1_trimmed.fastq

Latest Articles

Collapse

  • seqadmin
    Essential Discoveries and Tools in Epitranscriptomics
    by seqadmin


    The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist on Modified Bases...
    Yesterday, 07:01 AM
  • seqadmin
    Current Approaches to Protein Sequencing
    by seqadmin


    Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
    04-04-2024, 04:25 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
39 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
41 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 09:21 AM
0 responses
35 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-04-2024, 09:00 AM
0 responses
55 views
0 likes
Last Post seqadmin  
Working...
X