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Forum: Bioinformatics 03-30-2016, 07:32 PM
Replies: 5
Views: 1,909
Posted By DrWorm
Yeah, its mostly (if not all -- I just haven't...

Yeah, its mostly (if not all -- I just haven't tested thoroughly) #'s at the 3' end of reads. Seems like it shouldn't make much difference practically???
Forum: Bioinformatics 03-30-2016, 03:08 PM
Replies: 5
Views: 1,909
Posted By DrWorm
I'm told it was bcl2fastq2 2.17.

I'm told it was bcl2fastq2 2.17.
Forum: Bioinformatics 03-30-2016, 02:04 PM
Replies: 5
Views: 1,909
Posted By DrWorm
Comparing Cassava1.8.2 to bcl2fastq

Hello all,

A colleague of mine used Cassava1.8.2 and bcl2fastq to convert the same bcl file to fastq format. I was tasked with proving that the two resulting fastq files (again, the same data from...
Forum: Literature Watch 03-10-2016, 12:20 PM
Replies: 41
Views: 35,964
Posted By DrWorm
segmentation, ctd.

M CNVKit version is 0.7.8. R is installed, and I'm using PSCBS v0.61.0. Here's the output I get from the segmentation command.

to connect to socket /tmp/dbus-Hufo1aFYF5: Connection refused...
Forum: Literature Watch 03-09-2016, 01:30 PM
Replies: 41
Views: 35,964
Posted By DrWorm
errors in production of cns file

Hello all,

I'm having issues working through the install of CNVkit. I've pinpointed my issues to problems with the segment sub-command. When I try to run the test procedure, it dies with this...
Forum: Bioinformatics 03-03-2014, 01:24 PM
Replies: 7
Views: 4,521
Posted By DrWorm
Thank you!

Thank you!
Forum: Bioinformatics 03-03-2014, 12:19 PM
Replies: 7
Views: 4,521
Posted By DrWorm
Michael, I was hoping you might be able to answer...

Michael, I was hoping you might be able to answer one more related question...

I've decided that I need to control for batch variation since some of the parasites I'm studying were derived from...
Forum: Bioinformatics 02-20-2014, 06:48 PM
Replies: 7
Views: 4,521
Posted By DrWorm
Thanks for clearing that up. I'll take another...

Thanks for clearing that up. I'll take another look at my results with padj < 0.1 or 0.05.

I really appreciate your help! Thanks again for replying to my question.
Forum: Bioinformatics 02-20-2014, 03:14 PM
Replies: 7
Views: 4,521
Posted By DrWorm
Thanks so much for your reply! Just to be...

Thanks so much for your reply!

Just to be 100% sure...
I run the DESeq function just as you demonstrated, then I grab the results:
res <- results(dds)
Any gene with an adjusted p-value less...
Forum: Bioinformatics 02-19-2014, 12:38 PM
Replies: 7
Views: 4,521
Posted By DrWorm
Differential gene expression across life cycle with DESeq2

I'm trying to study gene expression across the life cycle of a nematode using DESeq2. We've sequenced eggs, L1, L2, L3, L4, L5, and adults. I've figured out how to do stage v. stage comparisons...
Forum: Bioinformatics 07-19-2013, 06:40 AM
Replies: 2
Views: 1,730
Posted By DrWorm
I believe we're using Python 2.6.5. I'll request...

I believe we're using Python 2.6.5. I'll request an update and see if that makes a difference.

Thanks for the advice!!
Forum: Bioinformatics 06-26-2013, 12:10 PM
Replies: 3
Views: 1,956
Posted By DrWorm
And one more thing ... I've read that BWA gives...

And one more thing ...
I've read that BWA gives ambiguously mapped reads a quality of 0. Would I have to pull those reads out separately somehow?
Forum: Bioinformatics 06-26-2013, 12:07 PM
Replies: 3
Views: 1,956
Posted By DrWorm
That sounds like a good idea. Do you know the...

That sounds like a good idea. Do you know the range in the quality scores? What's a reasonable cutoff to ask for? Is -q 30 what you would suggest?
Forum: Bioinformatics 06-26-2013, 11:43 AM
Replies: 3
Views: 1,956
Posted By DrWorm
BWA mem reporting poor alignments

I've been using bwa mem to align illumina reads to contaminant genomic databases (ribosomal RNAs, gbbct, etc). I've noticed unusually high percentages of reads mapping to my contaminants (10% or...
Forum: Bioinformatics 06-26-2013, 11:33 AM
Replies: 2
Views: 1,730
Posted By DrWorm
seq_crumbs memory issues

Hey all,

I've been loving the seq_crumbs package for trimming and filtering my Illumina data, and was excited to download the latest update that can handle paired end data. Unfortunately, when I...
Forum: RNA Sequencing 04-30-2013, 01:51 PM
Replies: 1
Views: 1,359
Posted By DrWorm
I re-read this and wonder if the description of...

I re-read this and wonder if the description of my perl script is unclear. I basically counted anything that did NOT have an "*" in the 3rd column. I just didn't want anyone to think I was getting...
Forum: RNA Sequencing 04-30-2013, 01:48 PM
Replies: 1
Views: 1,359
Posted By DrWorm
BWA output

Hi all,

I'm trying to screen paired Illumina RNAseq reads against a database of putative contaminants prior to assembly. BWA (version 7.0.3a, in case it matters) ran beautifully. Now I'm trying to...
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