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sample index and barcode in deduplicated reads #32

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sneha-nishtala opened this issue Aug 4, 2020 · 2 comments
Closed

sample index and barcode in deduplicated reads #32

sneha-nishtala opened this issue Aug 4, 2020 · 2 comments

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@sneha-nishtala
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Hello,

I used Calib to deduplicate my paired end reads.
calib -f S1_R1.fastq -r S1_R2.fastq -o S1_Calib. -l1 17 -l2 0

I have 8 bases index and 9 bases barcode attached to R1 while nothing attached to R2. Now, After running Calib and calib_cons, I noticed that the 17 bases of index+barcode is still attached to my reads. Is there a way to strip this?

Thanks!
@baraaorabi
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Calib does not remove barcodes or indices from the reads. This simple awk script should do just that:

awk 'NR%2==0{print($0,18)} NR%2==1 {print $0}' final.R1.fastq > final.R1.trimmed.fastq

Note: Calib should work find with index+barcode but it might be an overkill. Consider splitting the reads by sample index first, and then running each sample separately with Calib.

@sneha-nishtala
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Got it, Thank you!

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@baraaorabi @sneha-nishtala