Question: Error in TRinity
0
gravatar for majeedaasim
22 months ago by
majeedaasim40
United States
majeedaasim40 wrote:

I downloaded the fastq files from EBI ENA and then ran TRinity on them. Following error is shown

Error, not recognizing read name formatting: [SRR1188607.1]

The files appear like this

@SRR1188607.1 HWI-ST915_0064:2:1101:1420:2104/1 GTCTCTTCGCACGCTTTCACTGTGAACGGTTCGGCATCGAGAAGGACGCAGTTCCTCTCCGGCTTGGACCAGTTTCTGGTGGCCACGGCTGCCCCCATCC + HDHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHFHFFHHHHHHHHEHEHHHHHHHGHHHED?EE=A@BACDDECCE@DB74?############ How to fix this issue

ADD COMMENTlink modified 22 months ago by genomax74k • written 22 months ago by majeedaasim40

Can it be another read has the same name?

ADD REPLYlink written 22 months ago by Yang0

Since your reaction is not an answer, but rather a question for more information, I have moved this to a comment for now.

ADD REPLYlink written 22 months ago by WouterDeCoster42k

Another read is having the name as

@SRR1188607.1 HWI-ST915_0064:2:1101:1420:2104/2 CAAGGAGACGCTCCATTGTTGAGACGTAGCCCTTGAGGACGTCCTCGTAGGGAATCTTGTCCTCGCAGGGTGCGAAGAAGGTGATGGTGG + HHHHHHHHHHHHHHHHHEFGDEHFHHHHHCHHHFFHHHEHGEHHHFEBDEHHHHFHHHHHHHHHHHFHHF=EFFEFHEFFGDFEBFCAFD

ADD REPLYlink written 22 months ago by majeedaasim40

It appears paired-end reads in a single file.

ADD REPLYlink written 22 months ago by Puli Chandramouli Reddy180

If you want to use fastq-dump then in addition to the command options @toralmanvar provided you should use -F to restore original Illumina headers. This will remove SRR1188607.1 from fastq headers, which is what Trinity is complaining about.

ADD REPLYlink modified 22 months ago • written 22 months ago by genomax74k
0
gravatar for toralmanvar
22 months ago by
toralmanvar820
toralmanvar820 wrote:

SRR1188607 is a paired-end data so you should get 2 files after converting .sra file to fastq. If this is not the case, then please rerun fastqdump. Command which I use for PE data is :

fastq-dump -I --split-files input_file.sra

Give a try.

ADD COMMENTlink modified 22 months ago by genomax74k • written 22 months ago by toralmanvar820

This will likely cause the same problem as the original issue since this command will not recover original Illumina fasta headers which appears to be what Trinity is complaining about.

ADD REPLYlink written 22 months ago by genomax74k
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