Question: How to take out sequences with barcode?
1
gravatar for suvratha
5 months ago by
suvratha20
Institute of Bioinformatics and Applied Biotechnology
suvratha20 wrote:

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!

ADD COMMENTlink modified 5 months ago by Ido Tamir5.0k • written 5 months ago by suvratha20

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

ADD REPLYlink modified 5 months ago • written 5 months ago by cpad011211k

this helped, thanks!

ADD REPLYlink written 5 months ago by suvratha20
0
gravatar for Ido Tamir
5 months ago by
Ido Tamir5.0k
Austria
Ido Tamir5.0k wrote:

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.

ADD COMMENTlink written 5 months ago by Ido Tamir5.0k

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.

ADD REPLYlink written 5 months ago by suvratha20
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