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Search: Posts Made By: cedance
Forum: Bioinformatics 06-26-2012, 05:37 AM
Replies: 2
Views: 1,554
Posted By cedance
Just run Cufflinks alone. Cufflinks provides a...

Just run Cufflinks alone. Cufflinks provides a transcript.gtf file which consists of all possible transcripts. You could use gffread (http://cufflinks.cbcb.umd.edu/gff.html) then and provide your...
Forum: Bioinformatics 05-25-2012, 03:00 AM
Replies: 9
Views: 2,558
Posted By cedance
@arvid, Unless the hypothesis itself is to test...

@arvid, Unless the hypothesis itself is to test the validity of the claim that "unique k-mers are solely attributed to sequencing errors"?
Forum: Bioinformatics 05-25-2012, 01:57 AM
Replies: 9
Views: 2,558
Posted By cedance
based on what distribution do you sample k-mers?...

based on what distribution do you sample k-mers? gamma?
Also could you attach a plot of your k-mer frequency distribution/histogram?
Forum: Bioinformatics 05-24-2012, 04:38 AM
Replies: 23
Views: 4,318
Posted By cedance
EGrassi, About the cleanup, Yes! However, its...

EGrassi, About the cleanup, Yes! However, its just to remember the next time I look at the code that I am computing the coordinates of the junctions at open intervals :).

I just dint want to...
Forum: Bioinformatics 05-24-2012, 03:47 AM
Replies: 23
Views: 4,318
Posted By cedance
I map it on to the genome. I do not use picard. I...

I map it on to the genome. I do not use picard. I wrote a perl script using Bio::DB::Sam, with which its very easy to obtain all pairs and their inner distance. I take only uniquely mapped pairs and...
Forum: Bioinformatics 05-24-2012, 03:28 AM
Replies: 23
Views: 4,318
Posted By cedance
If you are curious about trying to estimate the...

If you are curious about trying to estimate the mean inner distance and its deviation, then you can take a look at the first reply here...
Forum: Bioinformatics 05-24-2012, 01:04 AM
Replies: 23
Views: 4,318
Posted By cedance
Do you also choose a value for --mate-std-dev?

Do you also choose a value for --mate-std-dev?
Forum: Bioinformatics 05-23-2012, 09:37 AM
Replies: 5
Views: 3,009
Posted By cedance
Excuse the bad terminology. The mapping I meant...

Excuse the bad terminology. The mapping I meant is not the generic "mapping" terminology associated with mapping reads to your genome. Rather a mapping in a "function" sense, or association, if you...
Forum: Bioinformatics 05-23-2012, 08:00 AM
Replies: 6
Views: 2,086
Posted By cedance
Okay it seems to be as I expected (and mentioned...

Okay it seems to be as I expected (and mentioned above). You can go here (http://picard.sourceforge.net/explain-flags.html) and type in the flag (2nd column) to see what the value indicates.

What...
Forum: Bioinformatics 05-23-2012, 06:00 AM
Replies: 6
Views: 2,086
Posted By cedance
Hi zxybl, It would be great if you could paste...

Hi zxybl,
It would be great if you could paste 1/a few lines of your sam file that seems to have issues.
Forum: Bioinformatics 05-22-2012, 01:19 PM
Replies: 38
Views: 25,634
Posted By cedance
Hi Colin, I have Maybe your indexing...

Hi Colin,
I have


Maybe your indexing was not complete?
Forum: Bioinformatics 05-22-2012, 12:04 PM
Replies: 5
Views: 3,009
Posted By cedance
What you are asking for, is essentially, another...

What you are asking for, is essentially, another mapping, isn't it? There should be a map of transcriptome to your genome constructed first (maybe easier with a genome annotation available? ) and...
Forum: Bioinformatics 05-22-2012, 11:48 AM
Replies: 6
Views: 2,086
Posted By cedance
The column 7 RNEXT tells you, in case of paired...

The column 7 RNEXT tells you, in case of paired end reads a "=" and in case of single end reads a "*" (or equivalently if a pair of your paired end read was removed pre-mapping by you or tophat as a...
Forum: Bioinformatics 05-18-2012, 05:19 AM
Replies: 3
Views: 1,730
Posted By cedance
Tophat does great job of mapping. So it should be...

Tophat does great job of mapping. So it should be alright.

As for SNP calling, there are plenty of softwares out there, but most of them are tuned not for RNA-seq I believe. Having said that, you...
Forum: Bioinformatics 05-18-2012, 05:06 AM
Replies: 38
Views: 25,634
Posted By cedance
Or build one from your reference genome...

Or build one from your reference genome (http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#the-bowtie2-build-indexer)
Forum: Bioinformatics 05-17-2012, 02:12 PM
Replies: 12
Views: 2,621
Posted By cedance
It wasn't clear what you were combining after,...

It wasn't clear what you were combining after, from your earlier post. Now it is.
Forum: Bioinformatics 05-17-2012, 02:00 PM
Replies: 12
Views: 2,621
Posted By cedance
chadn737, if you have biological replicates, its...

chadn737, if you have biological replicates, its better to keep them rather than merging and then finding genes that are differentially expressed.
Forum: Bioinformatics 05-17-2012, 01:30 PM
Replies: 23
Views: 4,318
Posted By cedance
I usually estimate the inner distance by mapping...

I usually estimate the inner distance by mapping reads using BWA and computing the mean inner distance and standard deviation. And for my samples, most of the time the reads overlap. The mean inner...
Forum: Bioinformatics 05-17-2012, 01:24 PM
Replies: 12
Views: 2,621
Posted By cedance
I meant, first merge all files, then map them....

I meant, first merge all files, then map them. Then split them back.
Yes, I just changed the header of each read of FASTQ (the first line of every read) to an ID that I can recognize which...
Forum: Bioinformatics 05-17-2012, 01:09 PM
Replies: 12
Views: 2,621
Posted By cedance
Yes, the idea is to retrieve back the replicates...

Yes, the idea is to retrieve back the replicates after mapping by merging them.
Forum: Bioinformatics 05-17-2012, 09:14 AM
Replies: 12
Views: 2,621
Posted By cedance
Sure, no problem. 25 million reads is plenty. I...

Sure, no problem. 25 million reads is plenty. I don't expect much of a difference.

I have not done it by supplying junctions from the merged run. Certainly that seems to be a nice idea.

What I...
Forum: Bioinformatics 05-17-2012, 08:40 AM
Replies: 12
Views: 2,621
Posted By cedance
I usually do this on samples where the sequencing...

I usually do this on samples where the sequencing depth is relatively less. If the depth of sequencing is around 30-40 million reads per sample, I don't see much of a difference between individual...
Forum: Bioinformatics 05-16-2012, 11:14 PM
Replies: 2
Views: 1,829
Posted By cedance
Quite late. Nevertheless, did you try SRMA...

Quite late. Nevertheless, did you try SRMA (http://genomebiology.com/2010/11/10/R99)?
Forum: Bioinformatics 04-27-2012, 02:38 PM
Replies: 12
Views: 9,139
Posted By cedance
swbarnes2, great! thank you. Just 1 more...

swbarnes2, great! thank you.
Just 1 more question. How about the NH:i:1 and XT:A:U optional flags in case of tophat and bwa? Of course its easy to just check for the unmapped read by doing a...
Forum: Bioinformatics 04-26-2012, 11:03 PM
Replies: 12
Views: 9,139
Posted By cedance
swbarnes2, Thanks for explaining the reason of...

swbarnes2, Thanks for explaining the reason of MAPQ error with regard to bwa. However, I don't follow this one. Could you please explain this part a bit more detailed? Thank you.
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