Hi,
I would like to know about the index used in the sample. I mean from the raw fastq file, I would like know the Illumina index read present in the raw fastq file. Is there any way to find that information from raw fastq file.
Kindly guide me. Thanks in advance.
2 answers
Your grep will also include every instance of CAGATC that's present in your reads (~1 per 4000 nucleotides of sequence). You want to parse only the read identifiers, which typically begin with '@HWI' .
Yes, the last field of the identifier is the index.
If you don't know the index sequence and/or the FASTQ contains multiple indices, you can use the following to get counts:
zcat NAME_OF_FASTQ | grep '^@H534' | cut -d : -f 10 | sort | uniq -c | sort -nr > indices.txt
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The example that you posted begins with @H534, not @HWI. Otherwise, the command should work.
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