Error in TRinity

Question

[majeedaasim]

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

[Yang]

Can it be another read has the same name?

[WouterDeCoster]

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

[majeedaasim]

Another read is having the name as

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

[Puli Chandramouli Reddy]

It appears paired-end reads in a single file.

[GenoMax]

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.

Answer 1

[Tm]

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.

[GenoMax]

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.