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Search: Posts Made By: sdarko
Forum: Bioinformatics 10-18-2017, 01:35 PM
Replies: 2
Views: 602
Posted By sdarko
Thanks for the tip. I grabbed the genes from...

Thanks for the tip.

I grabbed the genes from your link, subsetted my expression matrix, trained a random forest classifier using the gene set and known genders (with greater then 99% out-of-bag...
Forum: Bioinformatics 10-17-2017, 12:40 PM
Replies: 2
Views: 602
Posted By sdarko
Determining gender of donors from RNASeq data

Hi all,

I have, what I think, is an interesting question/problem.

We did some single-cell RNASeq (SMARTer prep, so whole transcripts not 3' tagging) on a group of samples. In healthy controls...
Forum: General 07-13-2015, 11:48 AM
Replies: 7
Views: 2,690
Posted By sdarko
Hi James, We are looking at ClarityLIMS for...

Hi James,

We are looking at ClarityLIMS for a small sequencing core. I'm interested to know how you liking using it an additional ~2 years after your initial post.

Thanks,
Sam
Forum: Illumina/Solexa 04-17-2013, 06:00 AM
Replies: 58
Views: 34,433
Posted By sdarko
Just wanted to chime in and say that we've seen...

Just wanted to chime in and say that we've seen run-to-run contamination too on our MiSeq.

After reading this post, I looked into it and found plenty of evidence.

Sam
Forum: Bioinformatics 04-11-2013, 10:48 AM
Replies: 6
Views: 2,755
Posted By sdarko
I think this would work for bowtie: bowtie -S...

I think this would work for bowtie:
bowtie -S -f -I 20 -X 7500 -a -m 1 -v 3 --rf build -1 reads_1.fasta -2 reads_2.fasta | samtools view -bSu - | samtools sort - aligned.sorted

I generally...
Forum: Bioinformatics 04-11-2013, 06:23 AM
Replies: 6
Views: 2,755
Posted By sdarko
bowtie2 -x $your_ref -U $in | samtools view -bSu...

bowtie2 -x $your_ref -U $in | samtools view -bSu - | samtools sort - $out
That's how I do it.
Forum: Bioinformatics 10-16-2012, 11:58 AM
Replies: 6
Views: 1,247
Posted By sdarko
In that same vein, did you do any adaptor...

In that same vein, did you do any adaptor trimming? That might be an issue if you haven't.

Sam
Forum: Bioinformatics 08-09-2012, 08:15 AM
Replies: 6
Views: 1,247
Posted By sdarko
Maybe SpliceMap...

Maybe SpliceMap (http://www.stanford.edu/group/wonglab/SpliceMap/)?

You know, you could always try TopHat. It's not like sequencing data goes bad after so many alignments :)
Forum: Bioinformatics 08-09-2012, 06:51 AM
Replies: 6
Views: 1,247
Posted By sdarko
You might want to try TopHat/Bowtie...

You might want to try TopHat/Bowtie (http://tophat.cbcb.umd.edu/index.html).

Alternatively, you can download all mRNA sequences from UCSC and align against that.

Sam
Forum: Bioinformatics 08-02-2012, 07:23 AM
Replies: 1
Views: 1,359
Posted By sdarko
The pre-release version of novoutil is able to do...

The pre-release version of novoutil is able to do what you need. I had the same problem.

http://www.novocraft.com/wiki/tiki-view_forum_thread.php?forumId=1&comments_parentId=691#threadId1

Sam
Forum: Bioinformatics 07-19-2012, 05:55 AM
Replies: 0
Views: 1,472
Posted By sdarko
Multi-sample VCF generated in GATK is not working with novoutil IUPAC

Hi,

We are trying to find SNPs in a few loci of interest in rhesus macaque. To that end, we have sequenced exome sequences and I've gone through the process of calling SNPs using GATK and I've...
Forum: RNA Sequencing 02-03-2012, 06:22 AM
Replies: 4
Views: 2,286
Posted By sdarko
I believe that you can use GATK and samtools on...

I believe that you can use GATK and samtools on RNA-Seq data.
Forum: Bioinformatics 01-05-2012, 05:11 AM
Replies: 6
Views: 4,506
Posted By sdarko
I think you're right.

I think you're right.
Forum: Bioinformatics 01-05-2012, 05:09 AM
Replies: 6
Views: 4,506
Posted By sdarko
Here is my script to run tophat and then kick off...

Here is my script to run tophat and then kick off cufflinks in SGE.

#!/bin/sh
#$ -N tophat_20111220_ucsc
#$ -S /bin/bash
#$ -q long.q
#$ -M [email protected]
#$ -m be
#$ -l h_vmem=4G
#$ -t 1-8
Forum: General 09-26-2011, 12:16 PM
Replies: 1
Views: 1,568
Posted By sdarko
Updated rhesus macaque genome?

Hi all,

I've been working with the rheMac2 assembly for the rhesus monkey and have found it to be woefully deficient in a number of regions. The rheMac2 assembly is also about 5 years old and had...
Forum: Bioinformatics 07-19-2011, 10:49 AM
Replies: 1
Views: 2,233
Posted By sdarko
TopHat Warning: Encountered reference sequence with only gaps

Hi,

I received the following warning during a tophat run earlier today.
[Tue Jul 19 11:55:37 2011] Indexing splices
Warning: Encountered reference sequence with only gaps
Warning: Encountered...
Forum: Bioinformatics 07-19-2011, 08:09 AM
Replies: 17
Views: 14,209
Posted By sdarko
Well, I figured out the problem. I put an extra...

Well, I figured out the problem. I put an extra tab between the chrom name and the second column in the gtf file when I renamed everything.

I fixed it and all is well.
Forum: Bioinformatics 07-19-2011, 07:32 AM
Replies: 17
Views: 14,209
Posted By sdarko
I want to make sure that I'm not messing up...

I want to make sure that I'm not messing up anything too basic first.

I grabbed the reference genome in fasta format from here --> ftp://ftp.ensembl.org/pub/release-63/fasta/homo_sapiens/dna/

I...
Forum: Bioinformatics 07-19-2011, 06:59 AM
Replies: 17
Views: 14,209
Posted By sdarko
Did you get your genome and gtf from the ensembl...

Did you get your genome and gtf from the ensembl website?

Other than renaming the gtf and fasta header entries so that they matched, was there anything else that you had to do to make the gtf...
Forum: Bioinformatics 07-15-2011, 09:36 AM
Replies: 4
Views: 1,479
Posted By sdarko
Command-line BLAST could work well.

Command-line BLAST could work well.
Forum: Bioinformatics 07-14-2011, 10:45 AM
Replies: 3
Views: 1,304
Posted By sdarko
How does cuffdiff/cufflinks determine "read type"?

From a recent cuffdiff run:
> Map Properties:
> Total Map Mass: 5798099.00
> Number of Multi-Reads: 0 (with 0 total hits)
> Read Type: 106bp x 106bp
> Fragment Length Distribution: Empirical...
Forum: Bioinformatics 07-14-2011, 06:03 AM
Replies: 17
Views: 14,209
Posted By sdarko
Thanks for the advise. I will try it out today.

Thanks for the advise. I will try it out today.
Forum: General 07-13-2011, 05:00 AM
Replies: 20
Views: 4,706
Posted By sdarko
Taking a random subset is on the agenda for...

Taking a random subset is on the agenda for today. Will let you know.
Forum: Bioinformatics 07-13-2011, 04:48 AM
Replies: 17
Views: 14,209
Posted By sdarko
Best source for GTF file for use with TopHat/Cufflinks

I've been grabbing the "refSeq genes" table (human, hg19) from UCSC in GTF file format for use with TopHat/Cufflinks.

I was just curious as to what everyone else is using and if I might find a...
Forum: General 07-13-2011, 04:45 AM
Replies: 20
Views: 4,706
Posted By sdarko
I think that one issue may be that in one...

I think that one issue may be that in one "identical" library we have ~ 4 million reads (with ~83% aligning to genome) while in the other "identical" library we have ~1 million reads (with ~71%...
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