Question: Paired end alignment issue
1
gravatar for aj123
3.4 years ago by
aj12380
United States
aj12380 wrote:

Hi,

I have paired end data which im trying to align using tophat:

tophat -r 200 -p 4 -o /.../Tophat_output/ -G /pathtogtf /pathtobowtieindexfiles Sample10_untrim1.fastq Sample10_untrim2.fastq

Im getting only one bam alignment file. Im not sure if I should be getting 2 bam files.

ADD COMMENTlink modified 3.4 years ago by Antonio R. Franco4.1k • written 3.4 years ago by aj12380
3
gravatar for Antonio R. Franco
3.4 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.1k wrote:

You should get the accepted bam file, and another one of unmapped sequences

But don't expect two bam accepted files, one for each of the paired sequences. You only get one

ADD COMMENTlink written 3.4 years ago by Antonio R. Franco4.1k
1

Does it matter if the unmapped sequences files are larger than the accepted hits.bam file?

ADD REPLYlink written 3.4 years ago by aj12380
2

Possibly. Look at the alignment_summary.txt file that should have been produced. That will tell you what happened during the alignments.

ADD REPLYlink written 3.4 years ago by genomax73k

yes thank you that answered my question.

ADD REPLYlink written 3.4 years ago by aj12380
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