Question: Subsampling aligned SAM/BAM files for RNA-seq analysis
0
gravatar for mohammedtoufiq91
13 months ago by
mohammedtoufiq91110 wrote:

Hi,

I would like to know if there are any specific tools to sub-sample aligned SAM or BAM files. What type of files could be considered for the sub-sampling sorted or unsorted SAM or BAM files.

Thank you, Toufiq

ADD COMMENTlink modified 13 months ago by WouterDeCoster43k • written 13 months ago by mohammedtoufiq91110
1
gravatar for WouterDeCoster
13 months ago by
Belgium
WouterDeCoster43k wrote:

You did not tell us anything about the aim of your analysis, which is probably important. For expression analysis I'd recommend subsampling the read counts. That is probably more efficient than subsampling alignments. First package that comes to mind is this R package: subseq

ADD COMMENTlink written 13 months ago by WouterDeCoster43k

We have generated a set of RNA-seq samples. These are human PE samples with read length of 150bp. We would like to identify the total number of genes that could be detected by reducing the number of reads to 1/2, 1/3rd and 1/4th. After this, identify the differentially expressed genes between the two conditions i.e. before/after treatment.

ADD REPLYlink written 13 months ago by mohammedtoufiq91110

There is a historical post. Check it out here.

ADD REPLYlink written 13 months ago by ivivek_ngs4.9k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1268 users visited in the last hour