Extracting Bar code From Fastq file

Question

[manojkumarbioinfo]

Hai,

I have a fastq file generated by Hiseq machine. i wish to extract the bar code of the sequence from the fastq files.

[Devon Ryan]

It's probably in the header and there's likely no reason to do so. It'd help if you provided a bit more detail.

[manojkumarbioinfo]

I'm posting my Header file of my fastq.

@M00196:24:000000000-AL55E:1:1101:14638:1425 1:N:0:4 
TCTACCTACGGGTAGTCCAGATCGGAAGAGCACACGTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAATGATATTCATTATATGTGACACGTCAATAGAAGCAATCAGCCAAGTGTCTGTAGCATGCTACTTTTTCTGTACAACAGACTTAATTTACTAAGCTATCCTATATGTTCTGCAGGCAGATGACTATCCACACCATATATTATTGTCTTATACATTCTTTAT 
+ 
CCCCCFFFFCCCEEGGGGGGGGHHGGGGHHHHHHHGHHHGHHHHHHFHHHHHHHGHHHEHHFGGHHHHGGGGGHHHHHHHFFFBC@GG@@>03344?44BB444444B44B32/0///3BB3@222222<@2202/1111<>0B2B/E/0/@B21111>F1B0000?12B11BFF>>>F1?////1B<>B2B>1B01B1<1

I'm running Qimme 2 for running cansava 1.8 the file name should be in the particular format for example L2S357_15_L001_R1_001.fastq.gz. The underscore-separated fields in this file name are the sample identifier, the barcode sequence or a barcode identifier, the lane number, the read number, and the set number.

I wrongly renamed the original file so i cant able to run my command.

[GenoMax]

In this example you appear to have lost the index sequence. It should be present in 1:N:0:4 in place where 4 is. I should look like 1:Y:18:ATCACG.

[cpad0112]

you have sample number (4) in place of index. By any chance, is this from base space v2? Refer to sample sheet from sequencing core for sample 4. manojkumarbioinfo.