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Forum: Bioinformatics 08-05-2014, 05:34 PM
Replies: 21
Views: 17,575
Posted By silentio
using -u when running samtools mpileup

using -u when running samtools mpileup
Forum: Bioinformatics 05-21-2013, 07:19 PM
Replies: 3
Views: 1,785
Posted By silentio
I found the problem. It is because of the fastq...

I found the problem. It is because of the fastq files. Normally a fastq file starts with '"@" in the ID line. However, before running bwa, I used another software to do some preprocessing, which...
Forum: Bioinformatics 05-19-2013, 07:00 PM
Replies: 3
Views: 1,785
Posted By silentio
BWA aligned sam file missing "QNAME" format

Hi all,
I am using BWA to align pair-end read to hg19 genome.
Command line are as follows:

bwa aln $ref_dir/hg19 -t 4 $work_dir/${sample}_human_1.fastq.gz > $sai_dir/${sample}_1.sai
bwa aln...
Forum: RNA Sequencing 07-02-2012, 01:27 AM
Replies: 1
Views: 998
Posted By silentio
In most cases, 16-17nt sRNAs are degraded from...

In most cases, 16-17nt sRNAs are degraded from longer sRNAs. Normally we splice sRNAs on gels which are 18-28nt in length for sequencing. Under that condition, it is unlikely sRNAs shorter than 17nt...
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