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Forum: Bioinformatics 04-22-2018, 10:00 PM
Replies: 676
Views: 176,849
Posted By susanklein
ah I see, thanks. So they are good alignments,...

ah I see, thanks. So they are good alignments, but to multiple sites. I'll have to rethink my strategy because I really should be keeping all alignments.

Thanks,

S.
Forum: Bioinformatics 04-15-2018, 05:37 PM
Replies: 676
Views: 176,849
Posted By susanklein
Ok I thought this was solved, but see below,...

Ok I thought this was solved, but see below, still getting sam file alignments with MAPQ=3, even though they actually look like good alignments. Is '3' given because you can't calculate a perfect hit...
Forum: Bioinformatics 04-12-2018, 10:22 PM
Replies: 676
Views: 176,849
Posted By susanklein
ambig=best worked, Thanks. S.

ambig=best worked, Thanks.

S.
Forum: Bioinformatics 04-11-2018, 08:40 PM
Replies: 676
Views: 176,849
Posted By susanklein
bbmap SAM output question

Hi,

I don't quite understand the SAM output of bbmap.sh

here is my line:

bbmap.sh ref=ref.fasta ambig=all nodisk=t nzo=t mappedonly=t outu=unmapped.fasta scafstats=stats.map in=reads.fastq ...
Forum: Bioinformatics 02-20-2018, 04:54 PM
Replies: 1
Views: 1,008
Posted By susanklein
Command line Blast.. not as good as it was?

Hi All,

I just have a general question for everyone who regularly uses command line blast with '-remote' i.e. using NCBI online databases. I'm using BLAST 2.6.0+ and I consistently get errors that...
Forum: Bioinformatics 02-12-2018, 02:45 PM
Replies: 104
Views: 32,956
Posted By susanklein
Yes, that worked. Thanks.

Yes, that worked. Thanks.
Forum: Bioinformatics 02-11-2018, 05:42 PM
Replies: 104
Views: 32,956
Posted By susanklein
Hi, yes I get your point. I have reduced it...

Hi,

yes I get your point. I have reduced it now.. Will update progress.

S.
Forum: Bioinformatics 02-08-2018, 06:34 PM
Replies: 104
Views: 32,956
Posted By susanklein
My mistake - I should have increased Xmx.. not...

My mistake - I should have increased Xmx.. not decreased it. It still seems to be stalling though RAM stays full but cpu activity drops to zero.. assembly never finishes.

S.
Forum: Bioinformatics 02-08-2018, 05:34 PM
Replies: 104
Views: 32,956
Posted By susanklein
Hi, I am getting a memory error with the...

Hi,

I am getting a memory error with the following:
tadpole.sh in=../fasta/2.fasta out=tad2.fa k=96 merge=t overwrite=t

The fasta is interleaved and has 57767162 reads. This is a metagenome...
Forum: Bioinformatics 10-18-2016, 03:52 PM
Replies: 1
Views: 812
Posted By susanklein
mycofier - new tool for ITS - anyone got it working yet?

https://www.ncbi.nlm.nih.gov/pubmed/27516337

https://github.com/ldelgado-serrano/mycofier
Having trouble getting this to work. Any one else using this program yet? It would be nice to ahve an...
Forum: Bioinformatics 08-26-2016, 05:42 PM
Replies: 676
Views: 176,849
Posted By susanklein
Hi, couldn't you just do it the other way...

Hi,

couldn't you just do it the other way around, Have the pacbio as ref and may your short refs to it?

Although I don't understand why you refs are so short.


S.
Forum: Bioinformatics 07-06-2016, 06:00 AM
Replies: 676
Views: 176,849
Posted By susanklein
thanks, good to know bbmap should work, it is my...

thanks, good to know bbmap should work, it is my favourite mapper. I'll try those parameters.

S.
Forum: Bioinformatics 07-06-2016, 05:49 AM
Replies: 676
Views: 176,849
Posted By susanklein
miRNA

Hi,

has anyone used bbmap to map miRNAs to mirDB or similar. Any idea what settings would be best? I need to get count data.

Thanks,

S.
Forum: Bioinformatics 05-03-2016, 09:51 PM
Replies: 5
Views: 3,243
Posted By susanklein
This problem is still going on. I have it now and...

This problem is still going on. I have it now and followed your advice but it did not work... e.g.

tbl2asn -p 2882.fsa -t template.sbt -a s -j "[organism=Listeria monocytogenes]" -w comment.txt -y...
Forum: Bioinformatics 05-03-2016, 09:36 PM
Replies: 5
Views: 3,243
Posted By susanklein
This problem is still going on. I have it now and...

This problem is still going on. I have it now and followed your advice but it did not work... e.g.

tbl2asn -p 2882.fsa -t template.sbt -a s -j "[organism=Listeria monocytogenes]" -w comment.txt -y...
Forum: Bioinformatics 04-17-2016, 10:13 PM
Replies: 12
Views: 1,913
Posted By susanklein
Thanks, I'll try that. It does work in the...

Thanks, I'll try that. It does work in the windows version of R so for now I'm just using that. Updating R (as a module) in my debian machine is not straightforward..

S.
Forum: Bioinformatics 04-17-2016, 09:48 PM
Replies: 12
Views: 1,913
Posted By susanklein
is this because my version of R is too old...

is this because my version of R is too old perhaps?
Forum: Bioinformatics 04-17-2016, 09:42 PM
Replies: 12
Views: 1,913
Posted By susanklein
But that's absurd!? I followed the installation...

But that's absurd!? I followed the installation instructions on the Bioconductor site:
https://bioconductor.org/packages/release/bioc/html/edgeR.html

source("http://bioconductor.org/biocLite.R")...
Forum: Bioinformatics 04-17-2016, 09:28 PM
Replies: 12
Views: 1,913
Posted By susanklein
...sorry have to wait 5 mins to reply (when did...

...sorry have to wait 5 mins to reply (when did that rule come in?)...

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base...
Forum: Bioinformatics 04-17-2016, 09:20 PM
Replies: 12
Views: 1,913
Posted By susanklein
yes, done that.

yes, done that.
Forum: Bioinformatics 04-17-2016, 07:06 PM
Replies: 12
Views: 1,913
Posted By susanklein
actually.. it wasn't it.. I just tried it out and...

actually.. it wasn't it.. I just tried it out and still getting

> fit <- glmQLFit(y,design)
Error: could not find function "glmQLFit"


? anyone?

Thanks
Forum: Bioinformatics 04-15-2016, 01:08 AM
Replies: 12
Views: 1,913
Posted By susanklein
ah, yes, that was it, thanks!!

ah, yes, that was it, thanks!!
Forum: Bioinformatics 04-14-2016, 09:17 PM
Replies: 12
Views: 1,913
Posted By susanklein
EdgeR Error: could not find function "glmQLFit"

Hi,

anyone know why I get this error trying to use edgeR? I installed everything according to https://bioconductor.org/packages/release/bioc/html/edgeR.html but when I try out the example at...
Forum: Bioinformatics 04-13-2016, 05:22 PM
Replies: 8
Views: 1,186
Posted By susanklein
featureCounts works great. Thanks for the tip.

featureCounts works great. Thanks for the tip.
Forum: Bioinformatics 04-12-2016, 01:21 AM
Replies: 8
Views: 1,186
Posted By susanklein
which package is featureCounts from? I need to...

which package is featureCounts from? I need to script, preferably in python, to handle a large number of bam files, so its hard to interact with R (can't script in R). I guess I will have to learn R!...
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