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Search: Posts Made By: Mizzou55
Forum: Bioinformatics 04-19-2018, 10:36 AM
Replies: 3
Views: 583
Posted By Mizzou55
Does the --by option sum up the coverage for an...

Does the --by option sum up the coverage for an interval (10000), or does it provide the depth at each interval?
Forum: Bioinformatics 09-22-2016, 01:23 PM
Replies: 330
Views: 114,218
Posted By Mizzou55
Hi Brian, In this case I'm trying to trim...

Hi Brian,

In this case I'm trying to trim vector and low qual from Sanger (BAC End Seq) reads (~850bp) to run through SSPACE. Will your script have problems with this?
Forum: Bioinformatics 09-12-2016, 06:54 PM
Replies: 330
Views: 114,218
Posted By Mizzou55
Thanks for the quick response. I'll give it a try.

Thanks for the quick response. I'll give it a try.
Forum: Bioinformatics 09-09-2016, 12:04 PM
Replies: 330
Views: 114,218
Posted By Mizzou55
Hi, I'm trying to trim fasta reads w/ quals but...

Hi, I'm trying to trim fasta reads w/ quals but get this error.

Thanks,

Pat

~pminx/bin/bbmap/bbduk.sh in=Cat_BES_325_500.fasta qfin=Cat_BES_325_500.qual out=Cat_BES_325_500_trim.fa...
Forum: Bioinformatics 09-17-2014, 02:55 PM
Replies: 252
Views: 98,475
Posted By Mizzou55
Hi, Has anyone seen this problem, and know...

Hi,

Has anyone seen this problem, and know how to fix it. We were going to remove the offending reads, but the we don't know how to convert the read names in the Reads dir, back to the input read...
Forum: Bioinformatics 03-12-2010, 08:13 AM
Replies: 278
Views: 109,001
Posted By Mizzou55
For the worm genome we have 100bp reads and two...

For the worm genome we have 100bp reads and two inserts sizes; 300 and 400 PE's. We will have 30-40X. Assuming the heterozygosity issue is resolved you would anticipate better results than SOAP or...
Forum: Bioinformatics 03-11-2010, 05:37 PM
Replies: 278
Views: 109,001
Posted By Mizzou55
Any sort of limit to number of Illumina reads Ray...

Any sort of limit to number of Illumina reads Ray can handle? We were going to try it on a 200 Mb worm that's repetitive and has high heterozygosity. What do you think, too big?
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