Forum: Bioinformatics
03-17-2015, 04:41 AM
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Replies: 2
Views: 1,886
Hi,
Unstranded library of RNASeq can have...
Hi,
Unstranded library of RNASeq can have strand bias, If yes then how can it be ruled out?
do we really look into it in case of fusion identification using tophat fusion?
Regards
Bharati
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Forum: Literature Watch
07-12-2013, 02:43 AM
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Replies: 5
Views: 4,834
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Forum: Bioinformatics
04-09-2013, 01:04 AM
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Replies: 23
Views: 43,501
Sorting bam file
How can I sort my bam file according to read headers. Kindly Reply soon.
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Forum: Bioinformatics
02-27-2013, 05:48 AM
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Replies: 3
Views: 1,439
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Forum: Bioinformatics
02-27-2013, 04:36 AM
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Replies: 1
Views: 3,775
I got this error with cufflinks ...
I got this error with cufflinks
GffObj::getSpliced() error: improper genomic coordinate 19628622 on chrY for NR_028083
Same error (with the same coordinates) was there for two different samples,...
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Forum: Bioinformatics
02-27-2013, 04:35 AM
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Replies: 3
Views: 2,150
Even I got this error
GffObj::getSpliced()...
Even I got this error
GffObj::getSpliced() error: improper genomic coordinate 19628622 on chrY for NR_028083
Same error (with the same coordinates) was there for two different samples, is there...
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Forum: RNA Sequencing
02-27-2013, 04:21 AM
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Replies: 6
Views: 3,778
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Forum: RNA Sequencing
02-27-2013, 04:20 AM
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Replies: 1
Views: 1,845
Even I am unable to use sam2mrf provided by...
Even I am unable to use sam2mrf provided by prebuilt binaries of RSEQtools, can anybody pls help?
The command I tried was "sort -r file.sam | sam2mrf > file.mrf"
as specified in the manual for the...
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Forum: Bioinformatics
02-27-2013, 04:19 AM
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Replies: 2
Views: 1,723
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Forum: Bioinformatics
02-27-2013, 04:19 AM
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Replies: 2
Views: 2,190
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Forum: Bioinformatics
02-27-2013, 04:17 AM
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Replies: 3
Views: 1,439
I am unable to use sam2mrf of RSEQtools, can...
I am unable to use sam2mrf of RSEQtools, can anybody pls help?
The command I tried was "sort -r file.sam | sam2mrf > file.mrf"
as specified in the manual for the alignment file generated by tophat...
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Forum: Literature Watch
02-27-2013, 04:16 AM
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Replies: 1
Views: 2,603
I am unable to use sam2mrf of RSEQtools, can...
I am unable to use sam2mrf of RSEQtools, can anybody pls help?
The command I tried was "sort -r file.sam | sam2mrf > file.mrf"
as specified in the manual for the alignment file generated by tophat...
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Forum: Bioinformatics
12-11-2012, 03:26 AM
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Replies: 6
Views: 3,627
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Forum: Bioinformatics
12-11-2012, 03:24 AM
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Replies: 3
Views: 2,378
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Forum: Literature Watch
12-11-2012, 03:10 AM
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Replies: 5
Views: 4,834
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Forum: Bioinformatics
12-08-2012, 05:01 AM
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Replies: 11
Views: 4,177
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Forum: Bioinformatics
12-06-2012, 09:33 PM
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Replies: 11
Views: 4,177
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Forum: Bioinformatics
12-05-2012, 05:53 AM
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Replies: 11
Views: 4,177
table description in result.html
Hi
In the table description of result.html generated by tophat-fusion-post I am unable to understand the last line ie "If you follow the the 9th column, it shows coordinates "number1:number2" where...
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Forum: Bioinformatics
12-04-2012, 10:21 PM
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Replies: 11
Views: 4,177
Explanation for result.html
Hi NKAkers,
Can you please explain the result.html file generated by Tophat-fusion-post, As I am unable to correlate this (result.html) file with its potential_fusions.txt file.
Thanx
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Forum: Bioinformatics
12-04-2012, 10:09 PM
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Replies: 3
Views: 2,378
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Forum: Bioinformatics
11-08-2012, 03:05 AM
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Replies: 11
Views: 4,177
Hi NKAkers,
This is not the case always, as...
Hi NKAkers,
This is not the case always, as some of the reads having 133 and 54 or 6 and 66 or 17 and 259 or even 36 and 710 at their 9 and 10 columns respectively (as shown below). I am unable to...
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Forum: RNA Sequencing
11-03-2012, 05:08 AM
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Replies: 5
Views: 3,479
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Forum: Bioinformatics
11-03-2012, 05:02 AM
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Replies: 2
Views: 1,673
Even I am having the same question, to find...
Even I am having the same question, to find fusions can we find unmapped reads from the SAM file generated by tophat2 without fusion search OR we should go for whole fastq file with fusion search...
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Forum: Bioinformatics
11-03-2012, 04:02 AM
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Replies: 3
Views: 3,206
I would recommend illumina as it has more...
I would recommend illumina as it has more advanced and standardized protocol with high accuracy. Or u can refer
"Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on the Same...
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Forum: Bioinformatics
11-03-2012, 03:00 AM
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Replies: 9
Views: 4,623
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