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Forum: Bioinformatics 11-06-2017, 07:08 PM
Replies: 240
Views: 85,517
Posted By TomHarrop
Hi Brian & others, I tried to run bbnorm...

Hi Brian & others,

I tried to run bbnorm with a kmer size of 99, but it crashed with the following error:

Exception in thread "Thread-371" Exception in thread "Thread-357" Exception in thread...
Forum: Bioinformatics 09-11-2017, 02:35 PM
Replies: 240
Views: 85,517
Posted By TomHarrop
Great, thanks!

Great, thanks!
Forum: Bioinformatics 09-11-2017, 02:21 PM
Replies: 240
Views: 85,517
Posted By TomHarrop
Can BBmap remove reads containing homopolymers?

Hi BBmap-ers,

Say I want to remove reads with more than 5 consecutive identical nucleotides. Is there a homopolymer/ polyX filtering option with BBDuk or reformat.sh?

Thanks!

Tom
Forum: Bioinformatics 05-31-2017, 06:12 PM
Replies: 240
Views: 85,517
Posted By TomHarrop
Hi Brian, I'm using reformat.sh to play...

Hi Brian,

I'm using reformat.sh to play around with some Nanopore reads. Is there any way to get the histograms (e.g. mhist, qhist, bhist) to track longer reads, like the `max` parameter in...
Forum: Bioinformatics 04-25-2017, 06:41 PM
Replies: 20
Views: 7,871
Posted By TomHarrop
Thanks for the suggestions. It's a TruSeq...

Thanks for the suggestions.

It's a TruSeq PCR-free library with an insert size around 470 bp according to the BioAnalyser. I did remove adaptors and contaminants with BBDuk2 (adapters.fa and...
Forum: Bioinformatics 04-25-2017, 05:50 PM
Replies: 20
Views: 7,871
Posted By TomHarrop
Great, thanks. How did you estimate the average...

Great, thanks. How did you estimate the average coverage from the % uniqueness? I know I can do it more accurately with BBNorm (which says read depth median at 55x) but I'm curious how you did it...
Forum: Bioinformatics 04-25-2017, 02:59 PM
Replies: 20
Views: 7,871
Posted By TomHarrop
Hi Brian, Thanks for this tool. What is...

Hi Brian,

Thanks for this tool.

What is the perfect_prob column in the results? I can't see it in the docs. Is it the "probability of correctness" for k-mers (reads?) in that bin based on...
Forum: Bioinformatics 12-27-2016, 11:12 PM
Replies: 7
Views: 2,913
Posted By TomHarrop
Thanks for the replies. Sorry about the slow...

Thanks for the replies. Sorry about the slow response, I missed the email notification over the holidays.

You're correct, the hits are mostly less than 60 bp, not the full read. I did try...
Forum: Bioinformatics 12-21-2016, 02:13 PM
Replies: 7
Views: 2,913
Posted By TomHarrop
I blastn-ed 1000 R1 and 1000 R2 reads from this...

I blastn-ed 1000 R1 and 1000 R2 reads from this library against the 'nt' database. For R1, I got 544 hits with an evalue < 1. 493 of them had usable taxon identifiers. From that I got 89 plant hits...
Forum: Bioinformatics 12-18-2016, 07:48 PM
Replies: 7
Views: 2,913
Posted By TomHarrop
Hi Brian, thanks for the reply. Contamination...

Hi Brian, thanks for the reply. Contamination sounds quite possible, I just BLASTed a random subset of the reads and got human, macaque, trees, zebrafish etc. as well as the occasional hit on other...
Forum: Bioinformatics 12-18-2016, 05:04 PM
Replies: 7
Views: 2,913
Posted By TomHarrop
No peak in BBNorm kmer-frequency histogram

Hi,

I'm working on de novo assembly of an insect genome. Our paired-end libraries were made from 10 ng of sheared DNA using a Rubicon ThruPLEX kit with 9 cycles of PCR. The bioanalyzer trace shows...
Forum: Bioinformatics 03-26-2015, 08:34 AM
Replies: 123
Views: 44,957
Posted By TomHarrop
Perfect, thanks.

Perfect, thanks.
Forum: Bioinformatics 03-26-2015, 03:13 AM
Replies: 123
Views: 44,957
Posted By TomHarrop
Hi again, I'm using the LRT with DESeq2 as...

Hi again,

I'm using the LRT with DESeq2 as follows.

> design(dds)
~batch + stage
> dds < - DESeq(dds, test = "LRT", reduced = ~ batch)

I see that I can access the calculated deviance for...
Forum: Illumina/Solexa 02-09-2015, 12:23 AM
Replies: 14
Views: 12,196
Posted By TomHarrop
Ah, this looks like it was exactly what I was...

Ah, this looks like it was exactly what I was missing. I was using --stranded=yes. Thanks for catching that and kmcarr for confirming. I switched to --stranded=reverse and now I have:
FS ...
Forum: Illumina/Solexa 02-03-2015, 04:10 AM
Replies: 14
Views: 12,196
Posted By TomHarrop
Help understanding the --library-type paramater for TruSeq Stranded llibraries

Sorry to drag this thread to the top again but I'm not sure I understand why the fr-firststrand parameter is recommended for mapping Illumina TruSeq Stranded libraries.

From my understanding of...
Forum: Bioinformatics 11-03-2014, 01:51 PM
Replies: 123
Views: 44,957
Posted By TomHarrop
Hi Michael, Forgot to thank you for your...

Hi Michael,

Forgot to thank you for your suggestions. Simple log-transformation with pseudocount reveals the differences in distribution of expression values in the degraded libraries.

Cheers,...
Forum: Bioinformatics 10-30-2014, 01:22 AM
Replies: 123
Views: 44,957
Posted By TomHarrop
Changes in r-log transformation?

Hi,

Sorry to dredge up this thread again but I have a question about the r-log transformation in the current version of DESeq2 (1.6.1).

I have a set of 8 libraries. Two of them were produced...
Forum: RNA Sequencing 07-28-2014, 06:15 AM
Replies: 2
Views: 1,012
Posted By TomHarrop
Problem solved! Not sure if anyone's reading...

Problem solved!

Not sure if anyone's reading this but I thought I'd do the right thing and post the answer in case someone googles it up in the future.

Right at the start of chromosome 9 of the...
Forum: RNA Sequencing 07-23-2014, 07:45 AM
Replies: 2
Views: 1,012
Posted By TomHarrop
A quick update. I'm still stumped by this issue....

A quick update. I'm still stumped by this issue. I did try re-mapping the reads with a different GTF file and genome fasta file, both of which I have used in previous analyses without problems. The...
Forum: RNA Sequencing 07-21-2014, 01:29 AM
Replies: 2
Views: 1,012
Posted By TomHarrop
Peak in transcript coverage profile

Hi all,

I'm analysing some RNASeq results using the tophat–htseq–DESeq2 pipeline. The libraries were prepared using polyA selection and some of our samples had low RINs, so I was checking the data...
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