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Search: Posts Made By: bharati
Forum: Bioinformatics 03-17-2015, 03:41 AM
Replies: 2
Views: 1,856
Posted By bharati
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
Forum: Literature Watch 07-12-2013, 01:43 AM
Replies: 5
Views: 4,760
Posted By bharati
Can u pls explain the ans u got.

Can u pls explain the ans u got.
Forum: Bioinformatics 04-09-2013, 12:04 AM
Replies: 23
Views: 43,179
Posted By bharati
Sorting bam file

How can I sort my bam file according to read headers. Kindly Reply soon.
Forum: Bioinformatics 02-27-2013, 04:48 AM
Replies: 3
Views: 1,419
Posted By bharati
Ya i specified the path for both the sam2mrf...

Ya i specified the path for both the sam2mrf script and that of the alignment file, even though it didnt work and terminates with the error "Invalid SAM entry: `"
Forum: Bioinformatics 02-27-2013, 03:36 AM
Replies: 1
Views: 3,737
Posted By bharati
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,...
Forum: Bioinformatics 02-27-2013, 03:35 AM
Replies: 3
Views: 2,052
Posted By bharati
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...
Forum: RNA Sequencing 02-27-2013, 03:21 AM
Replies: 6
Views: 3,705
Posted By bharati
I am unable to use sam2mrf provided by prebuilt...

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...
Forum: RNA Sequencing 02-27-2013, 03:20 AM
Replies: 1
Views: 1,807
Posted By bharati
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...
Forum: Bioinformatics 02-27-2013, 03:19 AM
Replies: 2
Views: 1,697
Posted By bharati
I am unable to use sam2mrf provided by prebuilt...

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...
Forum: Bioinformatics 02-27-2013, 03:19 AM
Replies: 2
Views: 2,153
Posted By bharati
I am unable to use sam2mrf provided by prebuilt...

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...
Forum: Bioinformatics 02-27-2013, 03:17 AM
Replies: 3
Views: 1,419
Posted By bharati
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...
Forum: Literature Watch 02-27-2013, 03:16 AM
Replies: 1
Views: 2,558
Posted By bharati
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...
Forum: Bioinformatics 12-11-2012, 02:26 AM
Replies: 6
Views: 3,574
Posted By bharati
Confusion between Spanning reads and spanning mate pairs

Can anybody please explain the difference between Spanning Reads and Spanning Mate pairs. As much I could understand Spanning reads are those reads which do not harbor the fusion point but Split...
Forum: Bioinformatics 12-11-2012, 02:24 AM
Replies: 3
Views: 2,334
Posted By bharati
Confusion between Spanning reads and spanning mate pairs

Hi NicoBxl

Can you please explain the difference between Spanning Reads and Spanning Mate pairs. As much I could understand Spanning reads are those reads which do not harbor the fusion point but...
Forum: Literature Watch 12-11-2012, 02:10 AM
Replies: 5
Views: 4,760
Posted By bharati
Confusion between Spanning reads and spanning mate pairs

Can anybody please explain the difference between Spanning Reads and Spanning Mate pairs. As much I could understand Spanning reads are those reads which do not harbor the fusion point but Split...
Forum: Bioinformatics 12-08-2012, 04:01 AM
Replies: 11
Views: 4,112
Posted By bharati
Confusion between Spanning reads and spanning mate pairs

Hi NKAkers,

What I understand is Spanning reads are those reads which do not harbor the fusion point but Split reads do harbor it, but Spanning mate pairs are those spanning reads which are...
Forum: Bioinformatics 12-06-2012, 08:33 PM
Replies: 11
Views: 4,112
Posted By bharati
Difference between Spanning Reads and Spanning Matepairs

hi
can you please explain the difference between Spanning Reads and Spanning Mate pairs. As much I could understand the number of Spanning mate pairs should be lesser than spanning reads, but this...
Forum: Bioinformatics 12-05-2012, 04:53 AM
Replies: 11
Views: 4,112
Posted By bharati
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...
Forum: Bioinformatics 12-04-2012, 09:21 PM
Replies: 11
Views: 4,112
Posted By bharati
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
Forum: Bioinformatics 12-04-2012, 09:09 PM
Replies: 3
Views: 2,334
Posted By bharati
tophat fusion post output

Can you please explain tophat fusion post output ie result.html file
Forum: Bioinformatics 11-08-2012, 02:05 AM
Replies: 11
Views: 4,112
Posted By bharati
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...
Forum: RNA Sequencing 11-03-2012, 04:08 AM
Replies: 5
Views: 3,421
Posted By bharati
Including TopHat there are many more tools which...

Including TopHat there are many more tools which can detect fusions both within and between chromosomes.
Forum: Bioinformatics 11-03-2012, 04:02 AM
Replies: 2
Views: 1,649
Posted By bharati
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...
Forum: Bioinformatics 11-03-2012, 03:02 AM
Replies: 3
Views: 3,171
Posted By bharati
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...
Forum: Bioinformatics 11-03-2012, 02:00 AM
Replies: 9
Views: 4,573
Posted By bharati
Hi NKAkers, sorry for my late reply. I only...

Hi NKAkers,
sorry for my late reply.
I only gave a single sample to filter false positives and it took less then a minute to complete and showed 0 filtered fusions.
Showing results 1 to 25 of 38

 


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