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Search: Posts Made By: dvanic
Forum: Bioinformatics 08-28-2016, 10:17 PM
Replies: 24
Views: 5,801
Posted By dvanic
Rsubread_1.20.6 or command line version...

Rsubread_1.20.6 or command line version subread-1.5.0-p1-Linux-x86_64
Forum: Bioinformatics 02-23-2016, 10:03 PM
Replies: 24
Views: 5,801
Posted By dvanic
Exclamation Error with long CIGARs

I'm trying to map some long reads (PacBio public human data), and use featureCounts to count reads to features (there are other ways of doing this, which I also use, but I'd like to use featureCounts...
Forum: RNA Sequencing 11-24-2014, 06:57 AM
Replies: 4
Views: 2,119
Posted By dvanic
Just as a note for other who may come across this...

Just as a note for other who may come across this post, I tried to use the above code with DESeq2 version 1.6.1, and got an error of


And at least for the version of DESeq2 I am using, the...
Forum: Bioinformatics 03-09-2014, 04:12 PM
Replies: 18
Views: 11,311
Posted By dvanic
HTSeq 0.6.1 Maximum alignment buffer size exceeded error

Hi! I'm usg HTSeq v 0.6.1 to count reads mapping to features (the htseq-count script). I'm getting a


18700000 SAM alignment record pairs processed.
Error occured when processing SAM input...
Forum: Bioinformatics 11-06-2013, 09:54 PM
Replies: 191
Views: 61,763
Posted By dvanic
Yes. I've posted on this...

Yes. I've posted on this here:http://seqanswers.com/forums/showpost.php?p=109498&postcount=50
Forum: Bioinformatics 09-09-2013, 08:44 PM
Replies: 4
Views: 3,046
Posted By dvanic
If you want to test whether you were lucky enough...

If you want to test whether you were lucky enough to get given a strand-specific library you can use the infer_experiment.py module of rseqc.

http://rseqc.sourceforge.net/

rseqc has a whole...
Forum: Bioinformatics 09-03-2013, 03:45 PM
Replies: 7
Views: 2,739
Posted By dvanic
Smile Thanks for your comments, Simon. My problem is a...

Thanks for your comments, Simon. My problem is a lot sillier than the wrong gtf - it's using the wrong denominator.

I did visualize the data with IGV and UCSC, and did see that most of my reads...
Forum: Bioinformatics 09-01-2013, 11:33 PM
Replies: 7
Views: 2,739
Posted By dvanic
Hi Simon! Thanks! I'm sure I'm using the...

Hi Simon!
Thanks!

I'm sure I'm using the right strand [have posted my results of how I chose the strand here: http://seqanswers.com/forums/showpost.php?p=109498&postcount=50 and I'm using the...
Forum: Bioinformatics 08-28-2013, 10:43 PM
Replies: 7
Views: 2,739
Posted By dvanic
HTSeq - how many reads map to features

Out of curiosity, how many reads are normally counted to features in your data?

I'm working with Illumina Random hexamer primed human PE RNA-Seq and using the gencode 17 annotation, and have...
Forum: Bioinformatics 07-15-2013, 04:10 PM
Replies: 2
Views: 2,569
Posted By dvanic
Have had exactly the same problem. Would really...

Have had exactly the same problem. Would really be lovely to know how to get around this bug....
Forum: Illumina/Solexa 07-03-2013, 09:33 PM
Replies: 58
Views: 41,460
Posted By dvanic
Post Sorry, but I think you're wrong!

I am using the currently available Illumina TrueSeq Stranded Total RNA Sample Preparation kit, the manual for which is Illumina part number 15031048 Rev. D. (googling that gives you the manual)
...
Forum: Illumina/Solexa 07-02-2013, 09:56 PM
Replies: 58
Views: 41,460
Posted By dvanic
And the correct option for htseq-count is...

And the correct option for htseq-count is --stranded=reverse?
Forum: Bioinformatics 03-27-2013, 11:59 PM
Replies: 13
Views: 4,939
Posted By dvanic
My point is that median exon length in human is...

My point is that median exon length in human is quite close to 100 nucleotides, and I work with 100bp PE reads.

So if I haven't managed to "hit" an exon junction with at least one read how...
Forum: Bioinformatics 03-27-2013, 04:33 PM
Replies: 13
Views: 4,939
Posted By dvanic
How confident can you be, though, that these...

How confident can you be, though, that these junctions are real? How well can you reconstruct these genes and their isoforms if you don't have enough reads that cover splice junctions?
Forum: RNA Sequencing 03-27-2013, 04:23 PM
Replies: 10
Views: 6,727
Posted By dvanic
It means that the biases of the technology have...

It means that the biases of the technology have been better characterized and methods of dealing with them described and validated.

The reason it's more "error prone" is that most people don't do...
Forum: RNA Sequencing 03-05-2013, 06:32 PM
Replies: 3
Views: 1,752
Posted By dvanic
We use BWA for small RNA-seq, and an added...

We use BWA for small RNA-seq, and an added advantage is that it will clip reads for you based on quality (i.e. dynamically). I would suggest trying it and seeing how many reads map.

Also, have you...
Forum: Bioinformatics 03-05-2013, 06:24 PM
Replies: 3
Views: 1,210
Posted By dvanic
UCSC table browser. If you go to UCSC and click...

UCSC table browser. If you go to UCSC and click on tables, and then use all regions that have no overlap with refseq as a custom track, followed by further intersecting that track to have no overlap...
Forum: Bioinformatics 03-05-2013, 05:47 PM
Replies: 5
Views: 1,624
Posted By dvanic
Uggh. Yet another reason not to use cufflinks......

Uggh. Yet another reason not to use cufflinks... but nothing quite tries to do what it does...
Forum: Bioinformatics 02-19-2013, 03:44 PM
Replies: 3
Views: 2,501
Posted By dvanic
Has anyone found the answer to this?

Has anyone found the answer to this?
Forum: Bioinformatics 02-18-2013, 05:18 PM
Replies: 13
Views: 4,939
Posted By dvanic
Hi! Yes, you're right, thank you for catching...

Hi! Yes, you're right, thank you for catching that. However, I would still argue that coverage search should be left off for longer Illumina reads and mammalian (human, mouse) transcriptomes: the...
Forum: Bioinformatics 02-10-2013, 02:10 PM
Replies: 5
Views: 1,624
Posted By dvanic
Question Cuffdiff time series with biological replicates

Hi! Sorry if this is a silly question, but when doing a time series comparison in cufflinks how do I specify that I have three replicates for each time point?



I have
-T first, first, first,...
Forum: Bioinformatics 02-03-2013, 12:02 AM
Replies: 13
Views: 4,939
Posted By dvanic
Thanks for the useful link, though I disagree...

Thanks for the useful link, though I disagree with the interpretation provided by the biostars poster!

From the tophat manual:


I've responded to this on biostars, but to repost here:
Hi!...
Forum: RNA Sequencing 01-28-2013, 07:26 PM
Replies: 67
Views: 68,914
Posted By dvanic
sdriscoll, have you tried doing the same analysis...

sdriscoll, have you tried doing the same analysis with the -g option (i.e cufflinks using reference transcripts as well as identifying novel ones) vs the -G one (which is only quantifying known...
Forum: RNA Sequencing 11-19-2012, 09:37 PM
Replies: 9
Views: 4,381
Posted By dvanic
Because some of my "non-primary" alignments look...

Because some of my "non-primary" alignments look quite good in IGV...
Forum: RNA Sequencing 11-19-2012, 09:36 PM
Replies: 9
Views: 4,381
Posted By dvanic
I am also quite interested in this! Still...

I am also quite interested in this! Still...
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