Question: Separate Broken Pairs
0
gravatar for Tom
7.1 years ago by
Tom0
Tom0 wrote:

I am currently preprocessing my paired-end reads and was wondering if there is an efficient way to remove broken pairs from my sequence file.

Thanks for the help.

illumina paired • 2.1k views
ADD COMMENTlink written 7.1 years ago by Tom0

Some more details would be good. What format is your RNA-seq data in and how has it been processed so far? And, how would you like to define "broken pairs"?

ADD REPLYlink written 7.1 years ago by Obi Griffith17k
0
gravatar for Istvan Albert
7.1 years ago by
Istvan Albert ♦♦ 80k
University Park, USA
Istvan Albert ♦♦ 80k wrote:

This post might help: Filtering paired end reads

ADD COMMENTlink written 7.1 years ago by Istvan Albert ♦♦ 80k
0
gravatar for Tom
7.1 years ago by
Tom0
Tom0 wrote:

It is in fastq format and following QC filtering with fastx I end up single reads that no longer have a pair. It seems that these single reads are messing up my assemblies in velvet. Recently, I tried using sickle to filter and it seems to have resolved the issue.

Thanks for the help.

ADD COMMENTlink modified 7.1 years ago • written 7.1 years ago by Tom0
0
gravatar for Ian
7.1 years ago by
Ian5.4k
University of Manchester, UK
Ian5.4k wrote:

Picard tools has a handy webpage for working out the meaning of SAM flags (and combinations of flags):

http://picard.sourceforge.net/explain-flags.html

These can be used with 'samtools view -f N', where N is the flag you want to filter your reads with.

E.g. to extract all the properly paired reads:

samtool view -S -f 2 -o proper-paired-reads.sam input.sam
ADD COMMENTlink written 7.1 years ago by Ian5.4k
0
gravatar for Tom
7.1 years ago by
Tom0
Tom0 wrote:

That is a great tool!

Cheers

ADD COMMENTlink written 7.1 years ago by Tom0
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