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@macmanes
Created May 9, 2014 13:44
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#Using Fastool downloaded with the most recent version of Trinity.
fastool --rev --illumina-trinity --to-fasta pero_left.2.fastq >> left.fa
Sequences parsed: 164311463
#I have a number of reads that are not appended with the /1 that is supposed to happen with --illumina-trinity
grep HSQ-7001360:67:H88RHADXX:1:1101:10000:20192 left.fa
>HSQ-7001360:67:H88RHADXX:1:1101:10000:20192
#This read seems to be properly formatted in the input file:
grep HSQ-7001360:67:H88RHADXX:1:1101:10000:20192 pero_left.2.fastq
@HSQ-7001360:67:H88RHADXX:1:1101:10000:20192 1:N:0:CCGTCC
#Most other reads are properly anotated with the /1 by fastool
head left.fa
>HSQ-7001360:67:H88RHADXX:1:1101:1448:2158/1
GGATATCTGACAATGTGACGTTTCTACATTTTTATATAAAGCAGATTTTTAAAATACAAGTGAGATAACATTTTCCTCTTGAAAATGATTATCTTACAAAAAAATAAACCTTGTATAAATTAAGCC
>HSQ-7001360:67:H88RHADXX:1:1101:1444:2179/1
ACGAGCCTACTTTACATCCGCCACTATAATTATCGCCATTCCAACAGGAGTAAAAGTATTCAGTTGATTAGCCACACTTCACGGAGGAAATATTAAATGATCACCAGCAATACTATGATCCCTAGG
>HSQ-7001360:67:H88RHADXX:1:1101:1526:2104/1
TATCATGTCTTCACTAGCAACAGGAAAATACACATGGTGTTTACTAAAATTGTTTACTACATTCAAATTCCCTTTTATTTTTTTAGTAGCCCAAGCTCTTGAGTTTTTCAAGACATTGTTTTCTGA
>HSQ-7001360:67:H88RHADXX:1:1101:1648:2136/1
TAAATGTTTTAGGCAGTCTAAGAACAAATGTAAAAGTAAAGACGCAGTAAAATGAATTGCTTGGTGTTCACTGCTCCATGTGTATCAAGCACAGCGGGAAACAAAACCCCC
#Not sure what the issue is here.
@fstrozzi
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fstrozzi commented May 9, 2014

Hi @macmanes,
could you send me a small FastQ with the sequences that are not appended ? Thanks

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