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Search: Posts Made By: sameet
Forum: Bioinformatics 06-12-2012, 10:19 AM
Replies: 1
Views: 2,344
Posted By sameet
What you are doing seems reasonable.

What you are doing seems reasonable.
Forum: Bioinformatics 06-12-2012, 05:20 AM
Replies: 15
Views: 9,294
Posted By sameet
Thanks Doris, I will try to rebuild the index and...

Thanks Doris, I will try to rebuild the index and see if that helps. I will update the post accordingly.
Forum: Bioinformatics 06-11-2012, 12:55 PM
Replies: 15
Views: 9,294
Posted By sameet
I still get the same error with even older...

I still get the same error with even older release of tophat.
Forum: Bioinformatics 06-11-2012, 11:50 AM
Replies: 2
Views: 1,358
Posted By sameet
Comparing data across different chemistries/throughputs.

Hi All,

I have data from 6 RNA-Seq runs that we did sometime last year on a HiSeq machine. A month ago we tried the new MiSeq sequencer and I have one data-set from the new machine. How valid...
Forum: Bioinformatics 06-11-2012, 11:31 AM
Replies: 15
Views: 9,294
Posted By sameet
The error persists!

I am using the latest tophat version, but the error persists. I am also trying with the oldest version available in our system to see if that works.
Forum: Bioinformatics 06-27-2011, 06:45 AM
Replies: 4
Views: 4,959
Posted By sameet
Is there any way to convert from *.wig* to *.bed*?

Is there any way to convert from *.wig* to *.bed*?
Forum: Bioinformatics 06-02-2011, 11:34 AM
Replies: 1
Views: 1,434
Posted By sameet
Repeat Masker with high throughput data

Hi,

I need to see how well my deep-sequencing data performs in different kind of repeat-regions in the human genome. Has anybody used RepeatMasker with high-throughput data?

Sameet
Forum: Bioinformatics 04-22-2011, 11:17 AM
Replies: 22
Views: 6,355
Posted By sameet
I got exact same error. What is worst, I was...

I got exact same error. What is worst, I was processing 8 files, I got this error for 5 files but TopHat worked okay for 3 files. This has me completely stumped.
Forum: Bioinformatics 12-24-2010, 03:04 AM
Replies: 9
Views: 11,416
Posted By sameet
Hi, I was thinking along same lines. But I...

Hi,
I was thinking along same lines. But I want to know how to handle situations when the same read maps to multiple locations, because this happens at a a pretty high high rate in my samples.
Forum: Bioinformatics 12-23-2010, 04:17 PM
Replies: 9
Views: 11,416
Posted By sameet
Hi, I am a bit confused. What should i use for...

Hi,
I am a bit confused. What should i use for N, total number of reads that mapped, or the unique number of reads that mapped. I cannot afford to discard the repeated reads because I have some...
Forum: RNA Sequencing 11-09-2010, 05:33 AM
Replies: 23
Views: 9,081
Posted By sameet
This solutions seems to be working perfectly. I...

This solutions seems to be working perfectly. I dont have an idea of how long it should take. But it did remove the adaptors and i am getting an output file that looks to contain a lot of reads...
Forum: RNA Sequencing 11-09-2010, 03:52 AM
Replies: 23
Views: 9,081
Posted By sameet
I think the following link is the most...

I think the following link is the most comprehensive list of all the primers as far as SOLEXA/Illumina is concerned.
...
Forum: RNA Sequencing 11-09-2010, 02:43 AM
Replies: 23
Views: 9,081
Posted By sameet
That was very helpful. I think this is exactly...

That was very helpful. I think this is exactly what I was looking for. Thank you.
Forum: RNA Sequencing 11-08-2010, 01:39 PM
Replies: 23
Views: 9,081
Posted By sameet
Hi, I have looked at the cutadpt. But in the...

Hi,
I have looked at the cutadpt. But in the help the sequence for the Illumina 5' primer is not given. Is that sequence or model for 5' primer already built-in in cutadapt. If not is that...
Forum: RNA Sequencing 11-05-2010, 11:03 AM
Replies: 23
Views: 9,081
Posted By sameet
Hi, Can you point me to the specific papers...

Hi,
Can you point me to the specific papers that you mention?
Forum: Illumina/Solexa 11-05-2010, 10:44 AM
Replies: 3
Views: 3,044
Posted By sameet
This thread, pretty much answers the question. ...

This thread, pretty much answers the question.

http://seqanswers.com/forums/showthread.php?t=418

--Sameet
Forum: Illumina/Solexa 11-05-2010, 10:21 AM
Replies: 3
Views: 3,044
Posted By sameet
Lightbulb How to convert old SOLEXA files to fastq?

Hi all,

I have some data in the old Solexa format, where there are a bunch of files in compressed form. There are .seq.txt and .prb files. Would it be possible to to convert these files to the...
Forum: RNA Sequencing 11-05-2010, 10:15 AM
Replies: 23
Views: 9,081
Posted By sameet
Hi, I was wondering about one more question....

Hi,

I was wondering about one more question. If the adaptors are trimmed, would you get the final 'usable' (for the lack of better word) sequences of different lengths?
Forum: RNA Sequencing 10-27-2010, 04:31 AM
Replies: 23
Views: 9,081
Posted By sameet
Hi Sparks, Thanks that was useful. I will...

Hi Sparks,

Thanks that was useful. I will look into this and keep you posted.
Forum: RNA Sequencing 10-26-2010, 09:01 AM
Replies: 23
Views: 9,081
Posted By sameet
@mmartin, I downloaded the code for cutadapt,...

@mmartin, I downloaded the code for cutadapt, however, it is not very clear how to use it with Illumina. Can you point me in correct direction?
Forum: RNA Sequencing 10-26-2010, 06:41 AM
Replies: 23
Views: 9,081
Posted By sameet
Can you give me the names of programs and...

Can you give me the names of programs and possible parameters for the adaptor trimming. I plan to use BowTie for the mapping of reads to the genome. I am only worried about one thing. As i am...
Forum: RNA Sequencing 10-26-2010, 05:13 AM
Replies: 23
Views: 9,081
Posted By sameet
Illumina GA-II. And because this is small RNA...

Illumina GA-II. And because this is small RNA during library preparation we used the RNA between 17 - 40 bases.
Forum: RNA Sequencing 10-26-2010, 04:46 AM
Replies: 23
Views: 9,081
Posted By sameet
Yes, our primary aim is to study changes in...

Yes, our primary aim is to study changes in micro-RNA profiles across a spectrum of genetic backgrounds.
Forum: RNA Sequencing 10-26-2010, 04:19 AM
Replies: 23
Views: 9,081
Posted By sameet
small RNA sequencing

Hi,

We recently obtained Illumina small-RNA RNA-seq data for S. pombe. I believe that the next step should be use of BowTie to map the reads back to the reference genome. Is there any specific...
Forum: Bioinformatics 05-07-2010, 09:44 AM
Replies: 19
Views: 3,889
Posted By sameet
@ThomasDoktor, thank you for the pointer. It...

@ThomasDoktor, thank you for the pointer. It does seem useful.
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