Forum: Bioinformatics
01-06-2013, 01:34 AM
|
|
Replies: 8
Views: 5,175
|
|
Forum: Bioinformatics
01-05-2013, 03:09 PM
|
|
Replies: 8
Views: 5,175
|
|
Forum: Bioinformatics
01-05-2013, 08:38 AM
|
|
Replies: 8
Views: 5,175
|
|
Forum: Bioinformatics
01-04-2013, 11:25 PM
|
|
Replies: 8
Views: 5,175
|
|
Forum: Academic/Non-Profit Jobs
09-15-2011, 02:28 PM
|
|
Replies: 2
Views: 3,506
|
|
Forum: Bioinformatics
08-06-2011, 06:00 PM
|
|
Replies: 5
Views: 7,257
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
|
|
Forum: Bioinformatics
12-04-2010, 03:40 PM
|
|
Replies: 19
Views: 17,233
|
|
Forum: Bioinformatics
12-02-2010, 04:22 PM
|
|
Replies: 14
Views: 3,756
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
|
|
Forum: Bioinformatics
11-18-2010, 08:49 PM
|
|
Replies: 2
Views: 2,866
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
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
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
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
|
|
Forum: Bioinformatics
11-09-2010, 05:56 PM
|
|
Replies: 0
Views: 934
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
|
|
Forum: Bioinformatics
11-07-2010, 11:51 PM
|
|
Replies: 4
Views: 3,540
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
|
|
Forum: Bioinformatics
11-07-2010, 09:52 PM
|
|
Replies: 17
Views: 6,924
|
|
Forum: Bioinformatics
11-07-2010, 06:39 PM
|
|
Replies: 17
Views: 6,924
|
|
Forum: Bioinformatics
10-29-2010, 02:37 AM
|
|
Replies: 6
Views: 2,048
|
|
Forum: Bioinformatics
10-28-2010, 07:58 PM
|
|
Replies: 0
Views: 1,890
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
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
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)...
|
