SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 49
Search took 0.00 seconds.
Search: Posts Made By: krespim
Forum: Bioinformatics 04-28-2017, 03:19 AM
Replies: 4
Views: 2,283
Posted By krespim
We are also planning some sRNA-seq in which we...

We are also planning some sRNA-seq in which we expect large differences in piRNA expression, and are thinking about these (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4538800/) spike-ins. However we...
Forum: Sample Prep / Library Generation 04-28-2017, 03:14 AM
Replies: 3
Views: 2,090
Posted By krespim
Our lab would also be interested. Did you find...

Our lab would also be interested. Did you find anything?
Forum: Epigenetics 12-20-2016, 01:31 AM
Replies: 3
Views: 3,355
Posted By krespim
I don't have an answer, but I am also very...

I don't have an answer, but I am also very interested in this topic. We are doing very similar experiments and there seems to be little out there on the analysis.
Forum: Bioinformatics 09-25-2015, 02:05 AM
Replies: 1
Views: 1,813
Posted By krespim
Hi Assa, if I understood you properly the...

Hi Assa,

if I understood you properly the issue is that you can't filter out junctions with less than N reads (let's say N = 5) from the junction files. You can do it with awk before the junction...
Forum: Bioinformatics 01-06-2015, 02:45 AM
Replies: 32
Views: 18,232
Posted By krespim
same in v2.0.13

I had the same experience with v2.0.13. Tophat stopped reporting the error when the 2 options, --no-discordant and --no-mixed, where removed.
Forum: RNA Sequencing 08-27-2014, 05:25 AM
Replies: 7
Views: 3,333
Posted By krespim
Update

I went back to my notes - because I had to run cuffdiff again - and the problem seems to occur when the annotation gft is not a cufflinks output or from iGenomes (not 100% sure about iGenomes...
Forum: Bioinformatics 05-23-2014, 03:54 AM
Replies: 15
Views: 4,111
Posted By krespim
Thanks for the reply Simon. Yep, this...

Thanks for the reply Simon.



Yep, this seems to be true. The samples are not mine, I am just the guy trying to make sense of the data.



In brief, experimentally, my collaborators are...
Forum: Bioinformatics 05-13-2014, 07:15 AM
Replies: 13
Views: 3,190
Posted By krespim
Thanks a lot for the suggestions. After posing...

Thanks a lot for the suggestions. After posing the question, I selected regions up to 500bpand also up to 1kb (always setting the -w parameter). And got a similar motifs with both which is...
Forum: Bioinformatics 05-09-2014, 11:11 AM
Replies: 15
Views: 4,111
Posted By krespim
The data comes from the junctions.bed files from...

The data comes from the junctions.bed files from tophat. I gave each junction a unique name (a combination of locus and junctions coordinates), created a matrix of counts by merging these...
Forum: Bioinformatics 05-08-2014, 06:54 AM
Replies: 15
Views: 4,111
Posted By krespim
de novo?

Great! I never used STAR, but do you remember if they used de novo junctions detected from the data?

Maybe is just my data that is too funky. The dispersion estimates are completely out of whack:...
Forum: Bioinformatics 05-07-2014, 12:05 AM
Replies: 13
Views: 3,190
Posted By krespim
Hi Simon, first of all thank you for the...

Hi Simon,

first of all thank you for the tool. I am now preparing to try it out but since my data is a tad tricky I was wondering if you could give some hints on how to best set-up the run.
...
Forum: Bioinformatics 05-06-2014, 08:17 AM
Replies: 0
Views: 988
Posted By krespim
Disparate numbers in IGV sashimi plot and junctions.bed

I trying to detect widespread splicing defects and amongst other things I ran tophat to find new splice junctions on my libraries (PE, 100 bases):



tophat -p 12 \
-r 200 --library-type...
Forum: Bioinformatics 05-06-2014, 06:41 AM
Replies: 15
Views: 4,111
Posted By krespim
Hi jmw86069. did you eventually try to run DEXseq...

Hi jmw86069. did you eventually try to run DEXseq with tophat junction.bed counts? I would be interested in knowing if it worked. I tried it with DESeq2, using each junction as separate identity and...
Forum: Bioinformatics 11-30-2013, 04:56 AM
Replies: 1
Views: 1,432
Posted By krespim
Gene expression of duplicate genes

I have some polyA(minus) RNAseq data and would like to quantify the gene expression of Pol3 transcribed genes. Well, quite a lot of these are duplicate loci (such as the RNU6) which makes it very...
Forum: Bioinformatics 11-14-2013, 01:02 AM
Replies: 4
Views: 1,559
Posted By krespim
Thankfully this is single read and I only have...

Thankfully this is single read and I only have the flag "0" and "16" on that field :)
Forum: Bioinformatics 11-14-2013, 12:54 AM
Replies: 4
Views: 1,559
Posted By krespim
also in awk

Thanks a lot dpryan. In the mean time some folks in lab helped to come up with a awk solution:

#!/usr/bin/awk -f

BEGIN{
FS="\t";OFS="\t";}
{
if($2=="16"){
$2="0";}
else{
Forum: Bioinformatics 11-13-2013, 11:16 PM
Replies: 4
Views: 1,559
Posted By krespim
Changing the strand in a Bam/Sam file

My sequencing data has been generated using the dUTP method, which means that when viewed in IGV or other browsers the reads are shown as being in the opposite strand from which they are generated....
Forum: Bioinformatics 07-01-2013, 07:04 AM
Replies: 27
Views: 5,005
Posted By krespim
Well, this is a bit out of my league now. I did...

Well, this is a bit out of my league now. I did found this which might help:
http://seqanswers.com/forums/showthread.php?t=12376

Otherwise send and email to the HTseq authors. Good luck.
Forum: Bioinformatics 06-30-2013, 11:50 PM
Replies: 27
Views: 5,005
Posted By krespim
Use samtools to sort your file

It should be no problem as all you have to do is download IGV to the cluster and add the folder where igv.jar is your PATH(or ask the admnistrator). 2nd step is: do you login remotely to the server?...
Forum: Bioinformatics 06-28-2013, 12:13 PM
Replies: 27
Views: 5,005
Posted By krespim
I misread the outpout and thought that none of...

I misread the outpout and thought that none of this reads were mapped - my bad. Nevertheless, 24M empty seems quite a bit to me. That said I also follow routinely your suggestion of looking at IGV...
Forum: Bioinformatics 06-28-2013, 10:57 AM
Replies: 27
Views: 5,005
Posted By krespim
Not having any read mapped suggests, to me, some...

Not having any read mapped suggests, to me, some issues with the annotation and/or with the parameters set for DEXSeq. I had that problem before when I was mapping using either the wrong annotation...
Forum: Bioinformatics 06-25-2013, 11:55 PM
Replies: 27
Views: 5,005
Posted By krespim
Still a damn good bioconductor package :) ...

Still a damn good bioconductor package :)

To be fair, I also had some difficulty in the beginning because my annotations/mappings were done with UCSC gene symbols and had to circumvent some...
Forum: Bioinformatics 06-25-2013, 11:17 PM
Replies: 27
Views: 5,005
Posted By krespim
Hi alittleboy, may I ask why you are sorting...

Hi alittleboy,

may I ask why you are sorting the SAM files that way? What I normally do is to keep everything in BAM file - as much as possible. So for DEXSeq read count I would index the BAM...
Forum: Bioinformatics 03-27-2013, 12:16 PM
Replies: 74
Views: 30,480
Posted By krespim
Based on my experience it can take a long time to...

Based on my experience it can take a long time to run. I think that you've mentioned that you are working with a small set of your data but it still may be worth running it in parallel.
Forum: RNA Sequencing 03-20-2013, 07:28 AM
Replies: 7
Views: 3,333
Posted By krespim
Well, I can't help much further but I can tell...

Well, I can't help much further but I can tell you what I end up doing. As I am working with species that have relative well annotated genomes/transcriptomes (Homo sapiens and Mus musculus), I forego...
Showing results 1 to 25 of 49

 


All times are GMT -8. The time now is 03:58 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO