How can I extract the overlap of the sequence data

Question

[190444373]

I have a sample of double-end sequencing 18-R-001_R1._fastq.gz,18-R-001_R2._fastq.gz, how to get the overlap of R1 and R2, and filter out the reads that R1 and R2 perfectly matched.(without mismatch)

[finswimmer]

Hello 190444373 ,

could you please explain why do you think this is a good idea?

fin swimmer

[190444373]

maybe my expression is unclear.so it looks a little bad.

Answer 1

[GenoMax]

You can use BBMerge from BBTools or FLASH to do the actual merging of the reads allowing for no mismatches.

• You can then use reformat.sh from BBMap suite to filter your data where the merged read is exactly the same length as R1/R2 (I am assuming your reads are all identical length to begin with and have not been trimmed, e.g. you could set minlength=n+1, n = length of R1/R2). That will filter out all reads where R1 and R2 perfectly match (your requirement).

• If R1/R2 perfectly match but have a shorter insert than the length of sequencing, those reads would also be removed by filter above.

[190444373]

Thank you for your reply, maybe my expression is unclear. For example, a 2x150bp read pair, the overlap is 50bp in the middle, I want this 50bp double-end sequence, and I want this 50bp R1 to be completely match 50bp R2. If the reads of R1R2 are not exactly matched, remove it.

[finswimmer]

This can be done with bbmerge to which genomax have linked.

$ bbmerge.sh in1=18-R-001_R1._fastq.gz in2=18-R-001_R2._fastq.gz out=overlap.fastq.gz pfilter=1 trimnonoverlapping=t

• in1 and in2 define the input files
• outdefine the output file
• pfilter=1 leads to merging only if there is no mismatch
• trimnonoverlapping=t trimm the parts of the reads that not overlap

[190444373]

Thank you so much, this is what I want.

[190444373]

If possible, I would like to ask if I can achieve my goal at the level of the bam file. For example, a bam file gets the read of the double-ended overlap, and R1R2 is also completely matched.

[GenoMax]

You will have to do the merging/trimming at the read level and then align the merged reads.

[190444373]

thank you for your reply.