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Forum: Bioinformatics 02-11-2014, 09:18 PM
Replies: 9
Views: 6,467
Posted By logicthief
Hi GenoMax, Thanks for your reply. Our...

Hi GenoMax,

Thanks for your reply.

Our library is prepared from amplicon.

I ran blat with default settings on the reads with more than 200 soft clipped reads. The first 18 columns of output...
Forum: Bioinformatics 02-09-2014, 12:21 PM
Replies: 9
Views: 6,467
Posted By logicthief
Thanks for your reply. 1. I'm checking the...

Thanks for your reply.

1. I'm checking the sequencing chemistry, we used phiX spike and V2 chemistry.

2. low complexity is an issue here, the average coverage is about 1200x, and we put...
Forum: Bioinformatics 02-08-2014, 11:28 AM
Replies: 9
Views: 6,467
Posted By logicthief
Overall distribution of quality score looks okay...

Overall distribution of quality score looks okay to me
2818

The distribution of quality for the reads with >200 soft clipping does look a little weird, though.
2819
Forum: Bioinformatics 02-07-2014, 03:55 PM
Replies: 9
Views: 6,467
Posted By logicthief
ps I think the adapter has been removed,...

ps I think the adapter has been removed, otherwise there will be much more soft clipped reads. Also the soft-clipping length shouldn't be that long if it is caused by adapter.
Forum: Bioinformatics 02-07-2014, 03:52 PM
Replies: 9
Views: 6,467
Posted By logicthief
High Percentage of Soft Clipping, BWA-MEM, MiSeq

Hi everyone,

I have 1,377,239 paired reads, 250bp each, 82,486 of them have been soft clipped for more than 200bp (eg a read with CIGAR string like 150S30M70S), is this normal?

These data come...
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