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