How to take out sequences with barcode?

Question

[suvratha]

Hello,

https://www.ncbi.nlm.nih.gov/sra/SRX2791702[accn]

In the above link, the design section has barcode sequences, how do i get all the reads with each particular barcode?

I did try using grep '^<barcode sequence="">' from the fastq file. But as you can see the last column in the link is "no. of sequences" and when i try to count the number by using grep, I'm getting a different number. The number I get is not matching with what they have provided.

Am i using grep incorrectly? what is the position of these barcode sequences?

Thanks!

[cpad0112]

use GBS tools such as GBSX for extracting reads with defined bar codes. suvratha

[suvratha]

this helped, thanks!

Answer 1

[Ido Tamir]

You could have been more precise with the difference between your read numbers and the stated numbers. If the stated one is bigger in all samples, then its because often and by default demultiplexing is done with 1 mismatch, which grep can not do.

[suvratha]

grep gives more than the number mentioned. for e.g - one the mentioned numbers there is about 6.1k and grep gives me 13.5k.