Question: Tophat - getQRead() failed
0
gravatar for alexander.nash
4.4 years ago by
United Kingdom
alexander.nash0 wrote:

I am trying to align paired end read data to the zebrafish transcriptome and for each sample I encounter the following error in the tophat_reports step:

Error: singleton getQRead() failed for id# 1627678

(id# differs for each sample)

The command I used was:

/usr/bin/tophat --library-type fr-firststrand -p 8 -N 2 -o ../tophat_alignments/SRR372798 -G ../annotations/Danio_rerio.Zv9.75.gtf Zv9 SRR372798_1_val_1.fq SRR372798_2_val_2.fq

I can't seem to find any other reports of this error.

Does anyone have any idea what might be causing this?

rna-seq alignment latest • 1.9k views
ADD COMMENTlink modified 2.7 years ago by davichen10 • written 4.4 years ago by alexander.nash0

hi, I also meet this problem, had you solve it

ADD REPLYlink written 3.1 years ago by young yu0

I also have the same problem, running tophat v2.0.13. This error seems to make my input into tophat really small, 100000 reads or so out of the 30 million in the fastq.

Anyone run into how to fix the problem? Does using less or 1 core help?

ADD REPLYlink written 2.7 years ago by davichen10

Pretty late to the game, but hope this helps anyone who comes by

I had the same problem using v2.0.13 of TopHat. Changing to the latest TopHat version fixed the issue. No idea why but it worked. Also updated Bowtie too and was able to avoid error.

ADD REPLYlink written 2.7 years ago by davichen10
0
gravatar for davichen
2.7 years ago by
davichen10
davichen10 wrote:

Pretty late to the game, but hope this helps anyone who comes by

I had the same problem using v2.0.13 of TopHat. Changing to the latest TopHat version fixed the issue. No idea why but it worked. Also updated Bowtie too and was able to avoid error.

ADD COMMENTlink written 2.7 years ago by davichen10
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