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Forum: RNA Sequencing 12-09-2016, 11:25 AM
Replies: 0
Views: 1,142
Posted By akhattri
RNAseq of too degraded FFPE samples

I want to prepare RNAseq libraries with RNAs from FFPE samples. In the past I have used TruSeq Access kit and it worked well if DV200 was >30. As I have same samples that are too degraded I wonder if...
Forum: Bioinformatics 02-06-2016, 04:28 PM
Replies: 2
Views: 1,536
Posted By akhattri
What worked best for your data? let me know? ...

What worked best for your data? let me know?

Thanks
Forum: Bioinformatics 01-03-2014, 03:06 PM
Replies: 13
Views: 2,800
Posted By akhattri
hi there, As swbarnes2 said, I've included the...

hi there, As swbarnes2 said, I've included the command ,in my question above , that I used to run vfs.
I used the same test files provided with the software (vfs), hence, I've not included the...
Forum: Bioinformatics 01-02-2014, 02:37 PM
Replies: 3
Views: 1,951
Posted By akhattri
Viral Fusion Seq Error with the test data

hi There,
I am getting this error while running VFS (http://sourceforge.net/projects/viralfusionseq/) (VERSION: Revision 1250) on CentOS 5 release 5.10 (Final) system. After this error SSAKE also...
Forum: Bioinformatics 01-02-2014, 12:32 PM
Replies: 13
Views: 2,800
Posted By akhattri
hi there, I am also getting somewhat similar...

hi there, I am also getting somewhat similar error while running VFS (VERSION: Revision 1250) on CentOS 5 release 5.10 (Final) system. After this error SSAKE also fails. Please let me know how this...
Forum: Bioinformatics 11-01-2013, 05:18 PM
Replies: 2
Views: 2,924
Posted By akhattri
awk - need help comparing 2 files

I have two files for which I want to compare first 2 columns. What I need is if col1 & 2 of file 1 matches col 1 & 2 of file 2, print that line of file 2.

File 1:
chr1 1 A
chr1 2 T
chr1 3 C
...
Forum: Bioinformatics 10-25-2013, 10:26 PM
Replies: 2
Views: 1,932
Posted By akhattri
Thanks gringer. I found a post describing the...

Thanks gringer. I found a post describing the similar way to do it:

samtools view -H mybamfile.bam | sed -e 's/SM:X/SM:Y/' | samtools reheader - mybamfile.bam > mybamfile.reheadered.bam


I...
Forum: Bioinformatics 10-25-2013, 08:30 PM
Replies: 2
Views: 1,932
Posted By akhattri
Changing RGSM without changing any RGID, RGPL etc

Hi there,
I have a bam file which was created by merging the two bam files – each a different run of same sample. Somehow while adding the read group information I added the wrong sample name to it....
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