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Forum: RNA Sequencing 01-31-2018, 12:37 AM
Replies: 0
Views: 988
Posted By bruce01
Single Cell FACS before Sequencing

Hi all,

we are designing an experiment to compare a control vs. condition (diet based) in rats to trial the new BioRad/Illumina single cell RNAseq protocol. I am interested to know if there are...
Forum: Bioinformatics 07-04-2016, 05:46 AM
Replies: 2
Views: 529
Posted By bruce01
You could take just those positions from the BAM...

You could take just those positions from the BAM using samtools view, and call variants on this BAM, or if you use GATK you can specify --intervals/-L in BED format for the required positons. Depends...
Forum: Vendor Forum 06-18-2016, 07:51 AM
Replies: 8
Views: 5,215
Posted By bruce01
Owning data legally requires ultimate control and...

Owning data legally requires ultimate control and exclusive rights of use. Does Genos relinquish rights of use and all control of the data?
Forum: Bioinformatics 07-30-2015, 10:05 AM
Replies: 304
Views: 81,838
Posted By bruce01
Hi Brian, to clarify, I did have mink=5 for...

Hi Brian,

to clarify, I did have mink=5 for the rest of the runs based on my previous assertion that SNP, methylation would not be called in the first/final 5bp of a read, so the 'mm' would have...
Forum: Bioinformatics 07-30-2015, 07:56 AM
Replies: 304
Views: 81,838
Posted By bruce01
Hi Brian, thanks for the reply. I have gone...

Hi Brian,

thanks for the reply. I have gone about testing different kmer to see what they result in in terms of retained bases. My thinking was that lower kmer should result in retaining less...
Forum: Bioinformatics 07-29-2015, 04:33 AM
Replies: 304
Views: 81,838
Posted By bruce01
Hi Brian, I have started using BBDuk as it...

Hi Brian,

I have started using BBDuk as it seemed more well documented and supported than alternatives, and alternatives did not function as I expected. Thanks for writing these tools.

Earlier...
Forum: Bioinformatics 05-11-2015, 04:32 AM
Replies: 2
Views: 543
Posted By bruce01
See this discussion....

See this discussion. (http://sourceforge.net/p/bio-bwa/mailman/message/31052880/)

TLDR: if all fastq are from a single library, concatenate and align as single files, otherwise align individually...
Forum: Bioinformatics 05-07-2015, 05:38 AM
Replies: 646
Views: 149,775
Posted By bruce01
Thanks Felix, I have tried BisSNP but it runs...

Thanks Felix, I have tried BisSNP but it runs very slowly (so slow as to be unusable, trying to figure out why currently) and have read the MethylExtract paper but not yet gotten around to running it.
Forum: Bioinformatics 05-07-2015, 03:12 AM
Replies: 646
Views: 149,775
Posted By bruce01
Hi Felix, thanks for the reply, sorry I...

Hi Felix,

thanks for the reply, sorry I missed the section in the manual.

I have tried using methylation data for CNV, and comparing this to shallow WGS and also exome for same samples. Exome,...
Forum: Bioinformatics 05-07-2015, 02:07 AM
Replies: 646
Views: 149,775
Posted By bruce01
Hi Felix, firstly, thanks for Bismark, it is...

Hi Felix,

firstly, thanks for Bismark, it is a great tool. And secondly, I have read the entire thread here and searched elsewhere, so apologies if this is discussed elsewhere.

My issue is...
Forum: Bioinformatics 04-28-2015, 03:43 AM
Replies: 4
Views: 1,888
Posted By bruce01
The problem is you are using the vector...

The problem is you are using the vector 'c("no_feature"...)', which does not contain "__no_feature" etc. If you add them to the previous vector then they will also be removed.
Forum: Bioinformatics 04-28-2015, 02:23 AM
Replies: 4
Views: 1,888
Posted By bruce01
Here...

Here (http://dr-k-lo.blogspot.ie/2013/11/in-in-r-underused-in-operator.html) is a good overview of what %in% does.

noint actually contains only those c("no_feature"...) that are found in...
Forum: Bioinformatics 03-24-2015, 03:39 AM
Replies: 149
Views: 48,910
Posted By bruce01
This is my problem, I have samples where s=1,...

This is my problem, I have samples where s=1, which is incorrect based on the library prep protocol which was dUTP based, have more counts than s=2. This is from FFPE tumor samples, and so I expect...
Forum: Bioinformatics 03-24-2015, 02:49 AM
Replies: 149
Views: 48,910
Posted By bruce01
Sorry about the nomenclature, I have +/- in my...

Sorry about the nomenclature, I have +/- in my head as they are in GTF and that is how I denote it in there.

Can I ask your opinion on what way to run featureCounts with stranded libraries?...
Forum: Bioinformatics 03-24-2015, 02:03 AM
Replies: 149
Views: 48,910
Posted By bruce01
Hi Wei, that makes sense for s=0, of course....

Hi Wei,

that makes sense for s=0, of course. I suppose my real question is that if we know what strand the RNA originally comes from do we not always need to use s=1+2, seeing as some will be from...
Forum: Bioinformatics 03-23-2015, 04:47 AM
Replies: 149
Views: 48,910
Posted By bruce01
Strand issues

Hi Wei,

I have been using single end 50bp stranded library, and was getting low counts and losing quite a lot of data. I tried '-s =0, 1, 2' and found discrepancies with counts. I expected 1+2 to...
Forum: RNA Sequencing 03-05-2015, 05:40 AM
Replies: 2
Views: 1,185
Posted By bruce01
I am having to design multiple cell line...

I am having to design multiple cell line experiments having never done so before and have similar issues. I don't know much about cell culture but wanted to answer you with our strategy, maybe...
Forum: Genomic Resequencing 01-29-2015, 10:46 AM
Replies: 11
Views: 8,354
Posted By bruce01
I use(d) HaplotypeCaller which is now recommended...

I use(d) HaplotypeCaller which is now recommended by GATK support as the one to use in all circumstances.
Forum: RNA Sequencing 01-21-2015, 06:22 AM
Replies: 14
Views: 4,725
Posted By bruce01
Did you try sorting by name and see if it works?...

Did you try sorting by name and see if it works? TBH I ran the same thing as you about two weeks ago and didn't get this error; my STAR is f1 so may be worth posting to STAR Google group as I am...
Forum: RNA Sequencing 01-21-2015, 04:24 AM
Replies: 14
Views: 4,725
Posted By bruce01
'Found reads that are not properly paired....

'Found reads that are not properly paired. (missing mate or the mate is not the next read)'

'--outSAMtype BAM SortedByCoordinate'

So mate is not the next read necessarily if BAM is sorted by...
Forum: Bioinformatics 12-30-2014, 12:17 PM
Replies: 2
Views: 628
Posted By bruce01
I had considered that as the most realistic...

I had considered that as the most realistic option, just wondered if there was a way to use unknowns. Thanks for your input.
Forum: Bioinformatics 12-30-2014, 05:29 AM
Replies: 2
Views: 628
Posted By bruce01
DESeq2 unknown treatment option?

Hi all,

I am wondering how I can include 'unknown' treatment/condition of samples in my design. I have two factors, one is method of mRNA preparation (RiboZero or PolyA), the second is 'responder'...
Forum: Bioinformatics 12-18-2014, 01:47 PM
Replies: 3
Views: 695
Posted By bruce01
Oh, you want reads to sit in two concurrent...

Oh, you want reads to sit in two concurrent features, I misread and thought you just wanted to be within one feature. No tools I know to do that, but thats because I never wanted to do that.

What...
Forum: Bioinformatics 12-18-2014, 06:31 AM
Replies: 3
Views: 695
Posted By bruce01
BEdtools intersect ...

BEdtools intersect (http://bedtools.readthedocs.org/en/latest/content/tools/intersect.html) will do this, you need tab-separated input so:

sed 's/\-/\t/g' <gff_or_bed> | sed 's/\s */\t/g' >...
Forum: Bioinformatics 12-18-2014, 04:58 AM
Replies: 2
Views: 1,959
Posted By bruce01
http://seqanswers.com/forums/showthread.php?t=6169

http://seqanswers.com/forums/showthread.php?t=6169
Showing results 1 to 25 of 157

 


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