One error in SSPACE

northbio

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Join Date: Sep 2010

Posts: 4
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One error in SSPACE

08-17-2016, 12:28 AM

I've encounter a strange problem when using SSPACE v3.0. I found that reads dealed by SSPACE were as follows in one fasta file in standard_output/reads :

>read24410302
GCCTTATCGCCCAACCTCAGTGATAAACGTTACTAATGCTCCTGTGGCTGAATGGGAGCAAATCCCTGCAGCCAGGTTACAAAATCTTGTTGAAAGCCTTCCAAGAAGAGCGGACGCTGTTATAGCTGTGTATTAATGCC
>read24410302
GAGTATGTCCTCAAACCAGAGCTTTCAAACTGTGAGGCGTGATGAGGTAAAGATGTTGTGTGAGTTGAAAGGGCCAGTTATTGTAGTATGGCCCCACTGATTGACACAGTCAGCAGTAGTAGCAGCAGTAGTGGCACACA
>read24410303
CAGGACAGAATCTGAACAGAAATGAGTCCAGAAGGAGATGGCTGTCAAAGTGTTAGTATTTTCTGACAAGATTAGTGCTGATATGGTTAACTGATTAAATCAATACAATGAAAAATAATCAATTCCAAATATGATGGTCA
>read24410303
TGCAGACTTGGAAAGCTCATCCCAGGGAAGGAGTATGTTTTCCGTATCCGTGCTGAGAACCGCTTTGGCGTGTCAGACCCCATTCAGTCTGACAGAATGGTTGCCAAGTTCCCCTTTGGTAAGTTTAATTGAATTATGTC
>read24410304
>ST-E00291:98:HVL7GCCXX:4:1101:5731:38878/1
>read24410304
GGGCTTTAAATCAAAAATAACCTGTATCCATTTCTCTGGGTCACGTACTGTAAATAATGCATTTTTTGATTGCATTCCTGCAACCTGGAAAATGTTATTTGTAAAAGGAAATTCTTGAACAAAATACACTACCTCAGATT
>read24410305
>ST-E00291:98:HVL7GCCXX:4:1101:5629:38878/1
>read24410305
AAAGCTGCAGGCGACTGTGCGTCTGCAACATGCAGCACATACACATGCATCAAAGTGTACACGCTAATACACCT
>read24410306
>ST-E00291:98:HVL7GCCXX:4:1101:28260:11488/1
>read24410306
TTGCCTTTTCTTCCAGGCTTCTAAATTTAAAAAACACAGGACAAAATGTGCTAAATAGGGAGCACACGGTACCAAGAGAGGACCCTGCCTCAGAAGTTAATCTGCCGAGGGCTTTAGAACAGAGCAACACACTGCAGAGC
>read24410307
>ST-E00291:98:HVL7GCCXX:4:1101:6380:38878/1
>read24410307
ACTGAGGACAGTATCTGGTATCAAGTTAATCAGTAAGACCATTTTACTCGCTGCACTCTCATTAG

As you can see, suddenly the fasta file gave wrong format of fasta file. At this time, I checked the reads file I gave in libraries.txt. I found the origin of this error:

>ST-E00291:98:HVL7GCCXX:4:1101:5609:38878/1
GCCTTATCGCCCAACCTCAGTGATAAACGTTACTAATGCTCCTGTGGCTGAATGGGAGCAAATCCCTGCAGCCAGGTTACAAAATCTTGTTGAAAGCCTTCCAAGAAGAGCGGACGCTGTTATAGCTGTGTATTAATGCC
>ST-E00291:98:HVL7GCCXX:4:1101:27245:11488/1
CAGGACAGAATCTGAACAGAAATGAGTCCAGAAGGAGATGGCTGTCAAAGTGTTAGTATTTTCTGACAAGATTAGTGCTGATATGGTTAACTGATTAAATCAATACAATGAAAAATAATCAATTCCAAATATGATGGTCA
>ST-E00291:98:HVL7GCCXX:2:1101AGTCCCTCTGACCCTCATGTGTGGGTTTTCTAACTGTACTGTGAATAAG
>ST-E00291:98:HVL7GCCXX:4:1101:5731:38878/1
ATGAAACACCCAGAGTACAATACTGGTTAATACGATACTGAATACTGAGTATCACAACACAAACTGAACTTCAAACACAGAATTTGAAGCCCACCTGTGACCTGTTACCTGAATCACACAGATACATAGTACCATCAAGA
>ST-E00291:98:HVL7GCCXX:4:1101:5629:38878/1
GTACAGACACAGCGTGGGACAAAGCAACGTTAAACCGAGTTCAATTAAAGAAAATGTCAGTCAGTTATGGGCCCAAAGCTTCAAATGTTGCATTTATCTTAAAACGATGAACGACTGGAGATCTTAAGATGAACTTTCGC
>ST-E00291:98:HVL7GCCXX:4:1101:28260:11488/1
TATTATTATTACTATTATTTTATTAATATTATTACCATTACCATTACTATTATTTTAAATCTGTATGTGAAATTTGCATTGTGCTACTGTATGCCCCCCCCTCAACCCAACTGGTCGAGGCAGATGGCTGCCCACATTGA

The red sequence is the point.......
But the real real point I want to say is this fasta is produced by bowtie2, which I used --un-conc to output these unmapped reads.
So, Be careful to use it ......
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