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Hello,
I am a new user of ABySS. I have 50 Million Solexa 100bp paired-end transcriptome reads that I am intending to assemble de novo. Velvet could not handle my dataset, but my first run with ABySS worked. However, I have a hard time understanding the output.
I have 4 questions:
1) I could not find any documentation on the output files created. Can someone maybe direct me to a page where the various files are explained?
2) I also do not quite understand if ABySS considers the paired end reads for the alignment or not. Does someone know? I have run the "pe" mode.
3) What is the number of mismatches allowed in a read to still be assembled to a contig?
4) below I pasted a few contigs from the outfile that Abyss has created (i.e. xxx_contigs.fa)
>29036 60 1326
GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTCTG
>29037 61 114
CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGTTG
>29038 62 268
TCGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTGTG
>29039 60 1139
GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGCTG
>29040 61 51
CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGCCG
>29041 60 13
GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGCTT
>29042 61 183
CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGGTG
>29043 61 44
CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTCCG
>29044 61 70
CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTTTG
>29045 69 20
GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGCTCATAAATGCA
>29046 69 34
GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTCTCATAAATGCA
>29047 69 20
GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTCTTGTAAATGCA
It is quite clear that these reads are identical with the exception of a few single base mismatchs. Why are they not merged into a single contig?
Thanks so much for your help!
I am a new user of ABySS. I have 50 Million Solexa 100bp paired-end transcriptome reads that I am intending to assemble de novo. Velvet could not handle my dataset, but my first run with ABySS worked. However, I have a hard time understanding the output.
I have 4 questions:
1) I could not find any documentation on the output files created. Can someone maybe direct me to a page where the various files are explained?
2) I also do not quite understand if ABySS considers the paired end reads for the alignment or not. Does someone know? I have run the "pe" mode.
3) What is the number of mismatches allowed in a read to still be assembled to a contig?
4) below I pasted a few contigs from the outfile that Abyss has created (i.e. xxx_contigs.fa)
>29036 60 1326
GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTCTG
>29037 61 114
CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGTTG
>29038 62 268
TCGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTGTG
>29039 60 1139
GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGCTG
>29040 61 51
CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGCCG
>29041 60 13
GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGCTT
>29042 61 183
CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGGTG
>29043 61 44
CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTCCG
>29044 61 70
CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTTTG
>29045 69 20
GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGCTCATAAATGCA
>29046 69 34
GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTCTCATAAATGCA
>29047 69 20
GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTCTTGTAAATGCA
It is quite clear that these reads are identical with the exception of a few single base mismatchs. Why are they not merged into a single contig?
Thanks so much for your help!
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