User: Sjannie Lefevre

Reputation:
30
Status:
New User
Location:
Department of Biosciences, University of Oslo, Norway
Last seen:
2 weeks, 3 days ago
Joined:
1 year, 8 months ago
Email:
s*************@gmail.com

Posts by Sjannie Lefevre

<prev • 6 results • page 1 of 1 • next >
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Answer: A: samtools manipulation of bowtie output with suppressed fields
... Ah, I found the information about essential fields in SAM/BAM files (http://samtools.github.io/hts-specs/SAMv1.pdf), and it seems that 11 are mandatory, so that must be why samtools does not want to read a bam file with suppressed fields... But then I am really confused as to how one is expected to ...
written 17 days ago by Sjannie Lefevre30
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samtools manipulation of bowtie output with suppressed fields
... Hi I am trying to create alignments from an riboseq experiment using bowtie1 (Bowtie/1.2.2-foss-2018b) on a HPC Linux cluster. Goal is downstream analysis using the riboseqr package. Riboseqr expects sorted bam files created with '--suppress 1,6,7,8', or txt files (i.e. sam). However, when I inc ...
riboseq samtools bowtie riboseqr rna-seq written 17 days ago by Sjannie Lefevre30
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Comment: C: bowtie2 unmapped reads
... Apparantly, it is an issue with the -k > 1 and the slightly old version (2.2.9) of bowtie2 that I am using: https://github.com/BenLangmead/bowtie2/issues/37 ...
written 21 months ago by Sjannie Lefevre30
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Comment: C: bowtie2 unmapped reads
... Here is the stats reported by samtools flagstat: 8,099,514,442 + 0 in total (QC-passed reads + QC-failed reads) 6,387,576,753 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 8,099,514,442 + 0 mapped (100.00% : N/A) 1,711,937,689 + 0 paired in sequencing 857,336,664 + ...
written 21 months ago by Sjannie Lefevre30
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Comment: C: bowtie2 unmapped reads
... I counted the lines of the unzipped file. When I do the same for the original file, I get the correct number of reads, 954,299,926, for both R1 and R2. So I do not think that the counting method is the problem. Also, the files with all reads are 273Gb, while the files with the un-mapped reads are 17 ...
written 21 months ago by Sjannie Lefevre30
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bowtie2 unmapped reads
... Hi :) I have assembled paired-end reads (illumina strand-specific) using trinity with some different settings, and then merged these assemblies and done some filtering. I now want to assemble the un-mapped reads (pairs that do not map concordantly), and I therefore mapped the reads to the assembly ...
bowtie2 rna-seq assembly written 21 months ago by Sjannie Lefevre30 • updated 21 months ago by Devon Ryan94k

Latest awards to Sjannie Lefevre

Popular Question 5 weeks ago, created a question with more than 1,000 views. For bowtie2 unmapped reads
Popular Question 21 months ago, created a question with more than 1,000 views. For bowtie2 unmapped reads
Commentator 21 months ago, created a comment with at least 3 up-votes. For C: bowtie2 unmapped reads

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