Error in Seqtk output

Question

[Prasad]

Hi,

i have 2 fastq file (R1 and R2). The problem is R1 has 5 (not per se) sequence and R2 has 6. i want only those reads and its pair from R2 file. so i used seqtk

seqtk sample -s100 test_R1.fastq 5 >seq1

seqtk sample -s100 test_R2.fastq 5 >seq2

but i am not getting exact pairend reads from both file. is there any ready tool which does that

[piet]

What do you mean by 'exact pairend reads'? Paired-end reads from Illumina should ideally not overlap at all.

Answer 1

[Devon Ryan]

It's somewhat difficult to tell exactly what your situation is. If "test_R1.fastq" is out of sync with "test_R2.fastq", then sync them before proceeding (BBTools has a convenient function for that as I recall).

In any case, you can subsample pairs of fastq files with BBTools as well. That's described here: Select sequences from fastq.gz file

Answer 2

[SES]

You cannot sample two files and expect the reads to be paired if they have a different number of sequences. As Devon said, you need to pair the reads first. Here is a lightweight solution using Pairfq:

curl -sL git.io/pairfq_lite | perl - makepairs -f test_R1.fastq -r test_R2.fastq -fp test_R1_p.fastq -rp test_R2_p.fastq -fs test_R1_s.fastq -rs test_R2_s.fastq

Now you can sample the paired files and get what you expect.

seqtk sample -s100 test_R1_p.fastq 5 > test_R1_p_5.fastq
seqtk sample -s100 test_R2_p.fastq 5 > test_R2_p_5.fastq

There is inline documentation for above command so ./pairfq_lite will show you the usage, and there is more information about that specific command on the wiki online. If you have a lot of sequences and little memory, I would recommend installing the program from the link above and using the indexing method (if you use this approach).