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length of quality sequence and length of read do not match in fastq

I am trying to use cutadapt to filter low quality read from the paired end fastq files (paired end human exome sequence) . But im getting error In read named 'Run0016Lane6Tile1...': length of quality sequence and length of read do not match (1!=95). How should i deal with this?

sequencing alignment next-gen
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updated by mastal511 mastal511 • written by ifudontmind_plzz ifudontmind_plzz

Have you tried to look at the read in question (hint: use $ grep -A 3 Run0016Lane6Tile1...)? Has the data been through some other scan/trim program already?

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written by GenoMax GenoMax

I did not do any quality trimming on these fastq files. When i tried to run bwa aln on these fastq files, it failed after 820 sequences have been processed.

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written by ifudontmind_plzz ifudontmind_plzz

1 answer

Where did you get the fastq files from?

In the first instance, I would use grep to check whether there is actually something wrong with your file at that particular fastq record.

grep -n -A4 'Run0016Lane6Tile1..' Read1.fastq
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written by mastal511 mastal511

I got these fastq files from already published data. I could see at line 3272, the length of quality sequence and length of read do not match.

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written by ifudontmind_plzz ifudontmind_plzz

Either the file you downloaded is corrupt at source or your local copy is bad. You could try re-downloading the file and see if it fixes the problem. Otherwise you may need to take that record out .. if whatever you are trying to do will allow for that. Remember to remove the corresponding record from R2 file, if this is paired-end data.

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written by GenoMax GenoMax

I will try to do the transfer once more and check.

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written by ifudontmind_plzz ifudontmind_plzz

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