Hi all,
-beware for a potentially stupid question-
I am using Velvet for the first time in hope to get a better alignment in a chromosome than just using my regular 100 bp paired end Illumina reads. I am doing this because the region appears to have a lot of repeats/gaps with normal BWA alignment.
Based on what I've read I am trying out different Velvet parameters to get the best N50 score.
I am using BWA to align the contigs back to the reference (don't know if this is the best thing to do) so I can see if the alignment has improved...I believe bwa bwasw is for longer single reads so I thought this would be appropriate.
However I am stuck on the bwa aln command.
bwa aln -t 4 canfam3.fasta contigs.fa > contigs.sai
It works fine for my contig.fa file that was produced with hash length 21, but when I try with contig.fa produced with hash length 31 I get an error:
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 159.48 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 94738 sequences have been processed.
[bsw2_aln] read 0 sequences (0 bp)...
[samopen] SAM header is present: 40 sequences.
[sam_read1] reference 'SN:X LN:123869142
' is recognized as '*'.
[main_samview] truncated file.
I have looked around but haven't found anything helpful, so does anyone have any ideas ? Or can someone suggest a better way of doing this?
Thanks in advance !
-beware for a potentially stupid question-
I am using Velvet for the first time in hope to get a better alignment in a chromosome than just using my regular 100 bp paired end Illumina reads. I am doing this because the region appears to have a lot of repeats/gaps with normal BWA alignment.
Based on what I've read I am trying out different Velvet parameters to get the best N50 score.
I am using BWA to align the contigs back to the reference (don't know if this is the best thing to do) so I can see if the alignment has improved...I believe bwa bwasw is for longer single reads so I thought this would be appropriate.
However I am stuck on the bwa aln command.
bwa aln -t 4 canfam3.fasta contigs.fa > contigs.sai
It works fine for my contig.fa file that was produced with hash length 21, but when I try with contig.fa produced with hash length 31 I get an error:
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 159.48 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 94738 sequences have been processed.
[bsw2_aln] read 0 sequences (0 bp)...
[samopen] SAM header is present: 40 sequences.
[sam_read1] reference 'SN:X LN:123869142
' is recognized as '*'.
[main_samview] truncated file.
I have looked around but haven't found anything helpful, so does anyone have any ideas ? Or can someone suggest a better way of doing this?
Thanks in advance !
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