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

Question

[ifudontmind_plzz]

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?

[GenoMax]

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?

[ifudontmind_plzz]

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.

Answer 1

[mastal511]

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

[ifudontmind_plzz]

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.

[GenoMax]

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.

[ifudontmind_plzz]

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