tophat: qual length error after trimming

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7.3 years ago

zz105 ▴ 20

I did trimming with Trimmomatics v0.36 with parameter SLIDINGWINDOW:10:20 MINLEN:60, and I ran tophat and got this error:

prep_reads v2.1.1 (13b3420)
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gzip: /lustre/beagle2/xyang/NB/Target/RNAseq/FastQ_trim/SRR1559168_1.fastq.gz: unexpected end of file
Error: qual length (13) differs from seq length (101) for fastq record SRR1559168.54082770!

gzip: stdout: Broken pipe

Is there a tool to fix this?

RNA-Seq rna-seq software error • 1.5k views

ADD COMMENT • link updated 7.3 years ago by GenoMax 141k • written 7.3 years ago by zz105 ▴ 20

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Looks like you ended up with a corrupted file. There probably was an error generated during the trimmomatic run. Go back and look for it. Best option would be to redo the trimming. If your original sequence file is corrupt then you would need to redownload it.

ADD REPLY • link 7.3 years ago by GenoMax 141k

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Thanks again, this is another file that passed the fastqc step, so there is definitely something wrong in the trim process

ADD REPLY • link 7.3 years ago by zz105 ▴ 20

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