Paired End Reads file formatting question

[IMPERATOR]

Hello all,

I have a quick question about the format of the fastq files for paired end reads.

For each sample I have a R1 and R2 file. Should I concatenate the files to do the mapping?

If it is optional, what would the advantages of one file be?

Thanks for your time!!!~~~!!!

[dpryan]

No, keep them separate. You will normally feed the aligner both files at once. One of the points of paired-end sequencing is that you can use one read to aid in the mapping of the other.

[IMPERATOR]

No, keep them separate. You will normally feed the aligner both files at once. One of the points of paired-end sequencing is that you can use one read to aid in the mapping of the other.

Thanks!

Quick follow up, someone told me to merge is .bam files for each paired read before I perform mpileup.

Is this kosher?

Tusen Takk

[GenoMax]

Read the manuals for the aligners/samtools before asking this kind of questions

[dpryan]

That would be a VERY unusual thing to do unless you have a very good reason to do so. My knee-jerk reaction would be to tell you to simply ignore anything that person ever says, but perhaps you're doing a non-standard experiment.

[swbarnes2]

Thanks!

Quick follow up, someone told me to merge is .bam files for each paired read before I perform mpileup.

Is this kosher?

Tusen Takk

Merging two bams that really are the same sample is usually a good idea, but you have paired end data. You don't want to treat it like two separate single end files. Read the manuals for bwa or bowtie, or whatever you are using, and do what it says for paired end data. You won't have to merge the .bams, the software will do that for you when you give it paired end data.

[IMPERATOR]

Merging two bams that really are the same sample is usually a good idea, but you have paired end data. You don't want to treat it like two separate single end files. Read the manuals for bwa or bowtie, or whatever you are using, and do what it says for paired end data. You won't have to merge the .bams, the software will do that for you when you give it paired end data.

~THANKS~

I was actually reading up on bowtie before working on it and I should give it my paired end reads