Error Message: Rna-Seq Alignment

Question

[Pals]

Hi, I was aligning paired-end RNA-Seq data for two samples. First data set was okay but I got following error message for second data

Error: Encountered one or more spaces while parsing the quality string for read HWI-ST588:137:D1A8UACXX:5:2214:4742:11437 2:N:0:CGTACTAGTATCCTCT. If this is a FASTQ file with integer (non-ASCII-encoded) qualities, try re-running with the --integer-quals option. terminate called after throwing an instance of 'int'

Do you have any idea what's wrong with my data and what should I do to get rid of it?

Thanks!

[Mikael Huss]

What does the quality string for the read look like? It's the last line of four in the FASTQ entry.

[Pals]

how can I find that particular read in my file?

[Istvan Albert]

the command below will select the four lines after matching the read

grep -A 4 "D1A8UACXX:5:2214:4742:11437" yourfilehere

[Sukhi Singh]

-A is awesome :)

[Pals]

Thanks Istvan..

[Pals]

There seems to be problem with the read. It does not have complete quality line and not a + line at all. The problem is with one mate as the same read in another mate has all info. Probably I would need to copy the read with right info and replace the bad one?

[Istvan Albert]

seems like a corrupted/truncated file - see if the rest of the reads have the right format as well. Use combinations of cat -n to output line numbers and identify at what line does the problem occur - then use head and tail to cut both files at various line numbers to see what is going on

[Pals]

Yes, it was truncated probably while extracting the zipped file. when I re-extracted, there were no errors. Thanks!