Greetings to all!
I was recently given some sequencing data for a not yet sequenced organism, so I am trying a de-novo assembly with Velvet. This is the first time I've been working with sequencing data, so I have one important question (and lots of others, but we'll have time for those):
The data is FASTQ Illumina 1.3+ paired-end. I have shuffled the two files according to the Velvet manual, but I have a lot of low quality positions, for example:
@HWUSI-EAS1785_0222:5:1:16937:1092#NCCAAT/1
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTGAAAAAANNANNAAAAAA
AAGACANAAAANNAGA
+
hhhhhhhhhhhhhhhhhhhhhghhhhhhhhhhhhhhhhhhhahhhhhhhhhhfhhgfggdhhgadBBBBBBBBBBBBBBB
BBBBBBBBBBBBBBBB
@HWUSI-EAS1785_0222:5:1:16937:1092#NCCAAT/2
NNNNNNNNNNGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAACAGGAA
GAGGAAATATGAGAAG
+
BBBBBBBBBBLJJHK__________YYTYYYYYYYb____b_bb_YYYYY_______Z____BBBBBBBBBBBBBBBBBB
BBBBBBBBBBBBBBBB
I am thinking of trimming the low quality positions, but then the mate-pairs would have different sizes. Would this have an effect on the Velvet output? You know, garbage in, garbage out...
Thanks a lot, and really hoping for an answer..
I was recently given some sequencing data for a not yet sequenced organism, so I am trying a de-novo assembly with Velvet. This is the first time I've been working with sequencing data, so I have one important question (and lots of others, but we'll have time for those):
The data is FASTQ Illumina 1.3+ paired-end. I have shuffled the two files according to the Velvet manual, but I have a lot of low quality positions, for example:
@HWUSI-EAS1785_0222:5:1:16937:1092#NCCAAT/1
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTGAAAAAANNANNAAAAAA
AAGACANAAAANNAGA
+
hhhhhhhhhhhhhhhhhhhhhghhhhhhhhhhhhhhhhhhhahhhhhhhhhhfhhgfggdhhgadBBBBBBBBBBBBBBB
BBBBBBBBBBBBBBBB
@HWUSI-EAS1785_0222:5:1:16937:1092#NCCAAT/2
NNNNNNNNNNGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAACAGGAA
GAGGAAATATGAGAAG
+
BBBBBBBBBBLJJHK__________YYTYYYYYYYb____b_bb_YYYYY_______Z____BBBBBBBBBBBBBBBBBB
BBBBBBBBBBBBBBBB
I am thinking of trimming the low quality positions, but then the mate-pairs would have different sizes. Would this have an effect on the Velvet output? You know, garbage in, garbage out...
Thanks a lot, and really hoping for an answer..
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