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
Can it be another read has the same name?
Since your reaction is not an answer, but rather a question for more information, I have moved this to a comment for now.
Another read is having the name as
@SRR1188607.1 HWI-ST915_0064:2:1101:1420:2104/2 CAAGGAGACGCTCCATTGTTGAGACGTAGCCCTTGAGGACGTCCTCGTAGGGAATCTTGTCCTCGCAGGGTGCGAAGAAGGTGATGGTGG + HHHHHHHHHHHHHHHHHEFGDEHFHHHHHCHHHFFHHHEHGEHHHFEBDEHHHHFHHHHHHHHHHHFHHF=EFFEFHEFFGDFEBFCAFD
It appears paired-end reads in a single file.
If you want to use
fastq-dumpthen in addition to the command options @toralmanvar provided you should use
-Fto restore original Illumina headers. This will remove
SRR1188607.1from fastq headers, which is what Trinity is complaining about.