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Forum: Bioinformatics 04-18-2016, 07:07 AM
Replies: 1
Views: 898
Posted By epi
set VCF filter manually

Hi,
Anyone knows of a way to set VCF FILTER field to pass irrespective of existing value that exists (from VQSR or other sources).
Forum: Bioinformatics 02-18-2016, 07:20 AM
Replies: 1
Views: 891
Posted By epi
miRNA-Seq alignment rate

I have a 50bp SE mouse miRNA-Seq study, I did quality and adapter trimming, aligned to miRBase v21,

% of uniquely aligned reads is 30-50% across samples, 40% average
about 17-30% aligns...
Forum: Bioinformatics 07-09-2012, 09:41 AM
Replies: 3
Views: 3,938
Posted By epi
tophat seq length qual length mismatch error

I am getting a seq length-qual length mismatch with tophat (2.0.0 and 2.0.3). Has anyone seen this or knows possible remedy. Surprisingly same program with same input work fine on a different system....
Forum: Bioinformatics 06-21-2012, 06:55 AM
Replies: 22
Views: 9,070
Posted By epi
Same problem 50 bp PE reads Can anyone...

Same problem
50 bp PE reads

Can anyone please comment if you have any insights or any way to bypass it so far.
Forum: Bioinformatics 05-15-2012, 05:38 AM
Replies: 16
Views: 6,961
Posted By epi
Thanks for commenting here, it is good to know I...

Thanks for commenting here, it is good to know I am not the only one in the this boat. I have pinged Cole again, hope he writes something here.
Forum: RNA Sequencing 05-15-2012, 05:37 AM
Replies: 47
Views: 45,955
Posted By epi
Hi Cole, as reflected in the thread, it seems...

Hi Cole, as reflected in the thread, it seems this not an incorrect use.

From the cufflinks manual: -g option


I was wondering if there is any solution or resolution, as many others have...
Forum: Bioinformatics 05-11-2012, 12:10 PM
Replies: 16
Views: 9,402
Posted By epi
Nobody can imagine that after reading your...

Nobody can imagine that after reading your message.



There is no unanimous opinion, and I did not disagree with anything. It is obvious I do not have an opinion that is why I am asking this...
Forum: Bioinformatics 05-10-2012, 05:15 AM
Replies: 16
Views: 9,402
Posted By epi
Thanks for commenting analyst, I just don't care...

Thanks for commenting analyst, I just don't care about responses like Alex's. Unfortunately he is not the only person in public forums and in scientific world who like to get personal in scientific...
Forum: Bioinformatics 05-02-2012, 08:36 AM
Replies: 16
Views: 9,402
Posted By epi
In other words, if library corresponds to sample,...

In other words, if library corresponds to sample, which i believe is the case with the data I have, same sample run in multiple lanes should be merged and then aligned.
This clarifies a lot. I have...
Forum: Bioinformatics 05-02-2012, 05:08 AM
Replies: 16
Views: 9,402
Posted By epi
Nice to see the discussion. I guess it depends on...

Nice to see the discussion. I guess it depends on individual experiment how much of an issue PCR duplicates might be. Won't this be a good practice to always merge fastq before align to remove any...
Forum: Bioinformatics 04-30-2012, 06:33 AM
Replies: 16
Views: 9,402
Posted By epi
You point is well taken. But there is another...

You point is well taken. But there is another situation in addition, which is when you want only reads matching to genome at one place, not various. If you align in batches, you can not have this...
Forum: Bioinformatics 04-30-2012, 06:30 AM
Replies: 15
Views: 10,180
Posted By epi
I am facing the exact situation mentioned in this...

I am facing the exact situation mentioned in this thread, in fact i started a new since i was unaware. Simon your reply is useful, especially splice aligners. Whats your opinion on aligning and then...
Forum: Bioinformatics 04-30-2012, 05:53 AM
Replies: 16
Views: 9,402
Posted By epi
Thanks for response. But will the alignment be...

Thanks for response. But will the alignment be not different when aligned together or in isolation. eg unique matches
Forum: Bioinformatics 04-27-2012, 12:31 PM
Replies: 16
Views: 9,402
Posted By epi
aligning multiple fastq for the same sample

Hi everyone, I am trying to align fastq against reference with bowtie. The input data contains same sample run in multiple lanes, 2, 3 or 4, as is commonly the case when expected depth could not be...
Forum: Bioinformatics 03-15-2012, 08:40 AM
Replies: 16
Views: 6,961
Posted By epi
Hi Cole, Thanks again for replying. While your...

Hi Cole, Thanks again for replying. While your comment clarifies some things, it also raises some more question. First here is my command


cuffmerge -o test1 -g genes.gtf -p 10 -s ~/path/mm9...
Forum: Bioinformatics 03-12-2012, 09:20 AM
Replies: 3
Views: 2,252
Posted By epi
I generally agree with the person posted above....

I generally agree with the person posted above. However, I will factor in read length and reference genome. depending on those, you can still go ahead with your approach in a fraction of time it will...
Forum: Bioinformatics 03-12-2012, 07:48 AM
Replies: 16
Views: 6,961
Posted By epi
Thanks you all for replies, and I apologize if I...

Thanks you all for replies, and I apologize if I was panicking more than needed. Perhaps I should explain my question a bit further.

As I understand, -g adds new transcripts "in addition to"...
Forum: RNA Sequencing 03-09-2012, 08:09 AM
Replies: 47
Views: 45,955
Posted By epi
Using cuffdiff means you are coming from...

Using cuffdiff means you are coming from tophat-cufflinks-cuffmerge workflow. I have found that this workflow is bugged and mixes up gene annotations. It can not be said with 100% certainty if the...
Forum: Bioinformatics 03-05-2012, 06:09 AM
Replies: 16
Views: 6,961
Posted By epi
To all Cufflinks users and author, can anyone...

To all Cufflinks users and author, can anyone please comment if I have stated my problem clearly.

Unfortunately it may be a serious bug in this software, which is causing it to mix FPKMs between...
Forum: Bioinformatics 03-01-2012, 07:09 AM
Replies: 3
Views: 3,916
Posted By epi
It seems you applied a rigorous quality filter to...

It seems you applied a rigorous quality filter to make your reads 25bp, or this was not a particular good sequencing run. Anyways, try -v which rids you of seed length altogether.
Forum: Bioinformatics 03-01-2012, 07:05 AM
Replies: 5
Views: 2,365
Posted By epi
Sorry can't help you with your specific problem. ...

Sorry can't help you with your specific problem.

Though in my experience, bowtie works much better than bowtie2. Apart from some bugs, many options are missing (strata/unique alignments). I...
Forum: Bioinformatics 03-01-2012, 06:57 AM
Replies: 16
Views: 6,961
Posted By epi
Cufflinks annotation handling business

Help me understand if you know, or comment if you find similar

Cufflinks run with -g, using GTF (from illumina igenomes).



ORIGINAL ANNOTATION...
Forum: Bioinformatics 02-29-2012, 07:50 AM
Replies: 0
Views: 2,662
Posted By epi
running IGV from command line

I am new to IGV use. It invokes fine from command line, loads the genome by -g, but as soon as I do -b followed by bam file, it prints gibberish on command line and don't do anything else. Any...
Forum: Bioinformatics 02-29-2012, 07:47 AM
Replies: 21
Views: 10,255
Posted By epi
Hi Cole, Thanks for your post. I keep reading...

Hi Cole, Thanks for your post. I keep reading your comments here which are useful for many including me. I asked a similar question, with a twist, here:...
Forum: Bioinformatics 02-27-2012, 12:35 PM
Replies: 7
Views: 10,549
Posted By epi
Cufflinks FPKM range

I am observing high FPKMs for cufflinks result, as many of you.
After going through the literature, it seems small genes and upper-quartile normalizations may be involved. While I am finding this to...
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