Question: (Closed) tophat equal length problem
0
gravatar for HK
8 days ago by
HK20
HK20 wrote:

Hey,

I am running an RNA seq pipeline, all my samples gave the output after mapping except one and it gives an error:

prep_reads v2.1.1 (ecf7617)
---------------------------
Error: qual length (76) differs from seq length (45) for fastq record !

gzip: stdout: Broken pipe

Stange that all the other worked perfectly. Then i tried fastqc to check the quality and it shopped at 65% and gave the error:

Approx 55% complete for 102842-001-042_R1.fastq.gz
Approx 60% complete for 102842-001-042_R1.fastq.gz
Approx 65% complete for 102842-001-042_R1.fastq.gz
Failed to process file 102842-001-042_R1.fastq.gz
uk.ac.babraham.FastQC.Sequence.SequenceFormatException: Midline 'GACTGATTCGTCTGG                                                          AGTTACCATTCCCTGTGGCTC' didn't start with '+'
        at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:172)
        at uk.ac.babraham.FastQC.Sequence.FastQFile.next(FastQFile.java:125)
        at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java                                                          :76)
        at java.lang.Thread.run(Thread.java:701)

Now i am clueless, what to do. I did not do any trimming as all the pre-processing was done my the company who gave the sequencing samples.

fastqc equal length tophat • 60 views
ADD COMMENTlink written 8 days ago by HK20

Hello HK!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

ADD REPLYlink written 8 days ago by genomax34k

well i have read that thread , but did not get any solution from that. thats why i am posting again.

ADD REPLYlink written 8 days ago by HK20

You posted the same question twice. That is why I closed this copy so we don't have two parallel conversations.

ADD REPLYlink modified 8 days ago • written 8 days ago by genomax34k
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