SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 80
Search took 0.02 seconds.
Search: Posts Made By: repinementer
Forum: Bioinformatics 01-06-2013, 01:34 AM
Replies: 8
Views: 5,175
Posted By repinementer
If you look at any published studies (2010-12),...

If you look at any published studies (2010-12), you will typically see 80-90% but not ~100%. What thats tells ? Tophat always reports 100%. Something wrong isn't it ?
Forum: Bioinformatics 01-05-2013, 03:09 PM
Replies: 8
Views: 5,175
Posted By repinementer
99.93% mapping ? I think it is not referring...

99.93% mapping ? I think it is not referring 99.93% of your reads are mapped. 100% mapping is not possible or at least too good be true.
Forum: Bioinformatics 01-05-2013, 08:38 AM
Replies: 8
Views: 5,175
Posted By repinementer
that gives the no.of mapped loci but not mapped...

that gives the no.of mapped loci but not mapped reads.
Forum: Bioinformatics 01-04-2013, 11:25 PM
Replies: 8
Views: 5,175
Posted By repinementer
How to count number of mapped paired-end and single-end rna-seq reads

Does any one know know, how to count number of mapped paired-end and single-end rna-seq reads using BAM files.
It seems samtools idx stats does not give exactly mapped reads information ? Any...
Forum: Academic/Non-Profit Jobs 09-15-2011, 02:28 PM
Replies: 2
Views: 3,506
Posted By repinementer
I couldn't locate them

I couldn't locate them
Forum: Bioinformatics 08-06-2011, 06:00 PM
Replies: 5
Views: 7,257
Posted By repinementer
May I add another question. I have the same...

May I add another question. I have the same scenario. 2 different chipseq from 2 different experiments (one in brain and one in heart). brain chipseq has 10 million tags and heart 4 million tags. I...
Forum: Bioinformatics 07-14-2011, 02:01 AM
Replies: 16
Views: 5,732
Posted By repinementer
Hi Please send me also

send it to repinementer@gmail.com

Thanx a ton!!!!!!!!!!!!!
Forum: Bioinformatics 12-04-2010, 03:40 PM
Replies: 19
Views: 17,233
Posted By repinementer
shouldn't you go for normalized reads...

shouldn't you go for normalized reads visualization instead of raw reads(SAM/BAM) ?
Forum: Bioinformatics 12-02-2010, 04:22 PM
Replies: 14
Views: 3,756
Posted By repinementer
I tried index format but ntworking

I converted file.bam to to file.bam.bai by using samtools.
And i tried to open file.bam.bi index file using IGV. It throwing by saying SAM/BAM index files are not supported ?
Forum: Bioinformatics 11-18-2010, 10:51 PM
Replies: 2
Views: 2,866
Posted By repinementer
Yes you are right. There are no negative values....

Yes you are right. There are no negative values. The least i observed was 0. And the library was rRNA depleted one.
May I know the usual range of FPKM values people get ? And also where could I get...
Forum: Bioinformatics 11-18-2010, 08:49 PM
Replies: 2
Views: 2,866
Posted By repinementer
FPKM minimum and maximum values ?

I successfully ran cufflinks and my gene.expr and transcripts.gtf and others are showing FPKM values. Maximum I observed in my data is 444467 FPKM and minimum is <0.

Are my values are in correct...
Forum: Bioinformatics 11-14-2010, 09:03 PM
Replies: 2
Views: 3,599
Posted By repinementer
Tophat Multiple inputs and out puts

Hi

I have 5 fastq files. Is it possible to run tophat on every one at the same time and get 5 outputs with a single command ? [ SAM files ] ?

In general Tophat accepts multiple files and gives...
Forum: Bioinformatics 11-12-2010, 02:11 AM
Replies: 15
Views: 4,988
Posted By repinementer
Hi guys does any one know how to convert this...

Hi guys does any one know how to convert this format to SAM ?
Author of this paper mentioned this is SAM format but it is not working with Cufflinks.
And it is not looking like the SAM format...
Forum: Bioinformatics 11-09-2010, 06:20 PM
Replies: 4
Views: 3,540
Posted By repinementer
But the data I have is Illumina-single end. As...

But the data I have is Illumina-single end. As per my knowledge I lllumina still doesn't have strand specific data ??
Anyways I did what you said but no use. see below

after adding strand info...
Forum: Bioinformatics 11-09-2010, 06:01 PM
Replies: 17
Views: 6,924
Posted By repinementer
@bacdirector: Yes I would be happy to do that....

@bacdirector: Yes I would be happy to do that. COuld you please provide me the code. My SOLID .csfasta data format looks like this
Forum: Bioinformatics 11-09-2010, 05:56 PM
Replies: 0
Views: 934
Posted By repinementer
bowtie_output.map to tophat.sam

I have a bowtie formt like the below. Is there anyway to convert this to SAM format ?


head -6 GSM485524_NA19200_argonne.map ...
Forum: Bioinformatics 11-08-2010, 07:07 PM
Replies: 17
Views: 6,924
Posted By repinementer
but fr-secondstarand is meant for SOLID data...

but fr-secondstarand is meant for SOLID data right ?
Forum: Bioinformatics 11-07-2010, 11:51 PM
Replies: 4
Views: 3,540
Posted By repinementer
SAM to CUFFLINKS SAM format

Does any one know how to convert SAM to cufflinks SAM format ?
Even manual is fine I can write a simple code that converts manual to command line.
All I want to know is is the first sequence is...
Forum: Bioinformatics 11-07-2010, 10:07 PM
Replies: 17
Views: 6,924
Posted By repinementer
is around ~ 80 %

is around ~ 80 %
Forum: Bioinformatics 11-07-2010, 09:52 PM
Replies: 17
Views: 6,924
Posted By repinementer
Hmmm I already have results with Bioscope but I...

Hmmm I already have results with Bioscope but I want to run these by using Tophat with out giving any known refseq annotation in order to find new transcripts.

Anyone suggestions on Tophat/bowtie
Forum: Bioinformatics 11-07-2010, 06:39 PM
Replies: 17
Views: 6,924
Posted By repinementer
ABI-SOLID data with Bowtie-0.12.7 and TopHat-1.1.2

Hi guys.
I successfully ran Solid data (50 bp reads) with current bowtie and tophat versions. But surprisingly it gave the following stats. especially only 21% aligning results!. Any one have any...
Forum: Bioinformatics 10-29-2010, 02:37 AM
Replies: 6
Views: 2,048
Posted By repinementer
how did you setup bowtie and tophat

how did you setup bowtie and tophat
Forum: Bioinformatics 10-28-2010, 07:58 PM
Replies: 0
Views: 1,890
Posted By repinementer
Tophat mean inner distance error for SOLID data

Sorry I solved the above question.
Now I'm unable to detect bowtie, the same old error.
I learnt setting up path for tophat and bowtie previously and successfully installed and worked with them for...
Forum: Bioinformatics 08-22-2010, 11:45 PM
Replies: 14
Views: 3,756
Posted By repinementer
Yes same observed in my analysis.

After supplying known ensemblegenes.gtf and ensemble_junctions and --no-novel-juncs I observed few cases where I have seen exactly you mentioned.
Seems it is still giving false postives by taking...
Forum: Bioinformatics 08-21-2010, 04:33 AM
Replies: 16
Views: 4,906
Posted By repinementer
New version of MapSplice error

I just tested new version of Mapsplice and it throwed the following error


]$ python bin/mapsplice_segments.py MapSplice.cfg

[Fri Aug 20 17:29:24 2010] Beginning Mapsplice run (v1.13.6.1)...
Showing results 1 to 25 of 80

 


All times are GMT -8. The time now is 05:04 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO