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Search: Posts Made By: kumardeep
Forum: Bioinformatics 03-28-2015, 10:53 AM
Replies: 14
Views: 7,161
Posted By kumardeep
I am struggling with the alignment of my .dat...

I am struggling with the alignment of my .dat file (4Gb) with the reference build file hg19.dat. Both the dat files have been made using MosaikBuild
(i) MosaikBuild -fr hg19.fa -oa hg19.dat
(ii)...
Forum: Bioinformatics 09-25-2012, 03:47 AM
Replies: 6
Views: 11,482
Posted By kumardeep
Thanks Marloch...:)

Thanks Marloch...:)
Forum: Bioinformatics 09-25-2012, 03:08 AM
Replies: 6
Views: 11,482
Posted By kumardeep
How to fetch sequence from chromosome coordinates

Hi all
I have chromosome coordinates (e.g. 5233922 to 5235189 of chr18). how can I get the sequence corresponding to this region ?
Like this I have huge file containing chr1 to chr21 and chr X and...
Forum: Bioinformatics 09-25-2012, 02:54 AM
Replies: 0
Views: 778
Posted By kumardeep
RES file format interpretation for expression calculation

Dear all,
I was trying to analyze the expression data provided in RES formats.
My specific queries include:

(1) These absolute values are fold changes (over expression) or what ?
And are...
Forum: RNA Sequencing 09-04-2012, 02:51 AM
Replies: 0
Views: 1,566
Posted By kumardeep
How to differentiate driver mutations from common/random mutations and SNPs in cancer

Hi all,

I am working on RNA-seq data ( our own experimental data) for some cancer types of human. I want to know whether the genes found/mapped in the raw data have mutations significantly...
Forum: Bioinformatics 08-23-2012, 03:48 AM
Replies: 3
Views: 2,689
Posted By kumardeep
hi I got two solutions (1) Here is a...

hi
I got two solutions

(1) Here is a perl script to convert wig to a bedgraph format: http://genomewiki.ucsc.edu/images/9/9d/FixStepToBedGraph_pl.txt

(2) googling for wig2bed returns a...
Forum: Bioinformatics 07-02-2012, 09:50 PM
Replies: 3
Views: 2,689
Posted By kumardeep
Convert WIG file into Fasta file

Hi all

I have a *.wig file which contains some mutation information. This file is easily viewed from the IGV viewer. But I want to convert this file into FASTA file or some other file so that I...
Forum: Bioinformatics 06-23-2012, 01:46 AM
Replies: 1
Views: 2,391
Posted By kumardeep
Implementation of IGV or IGB tool on web page.

Hi all
I have aligned short reads on the refernce genomes and these are analysed by the IGV and IGB tools as standalone versions. But I want to implement these tools on my web page so that any user...
Forum: RNA Sequencing 05-10-2012, 09:55 PM
Replies: 1
Views: 2,901
Posted By kumardeep
Cuffmerge command giving error- TypeError: 'str' object is not callable

Hi all
I am merging the 1 test sample transcripts.gtf and 1 control sample transcripts.gtf files through cuffmerge via this command :

cufflinks-2.0.0.Linux_x86_64/cuffmerge -s ref-genomes/hg19.fa...
Forum: RNA Sequencing 05-10-2012, 01:59 AM
Replies: 1
Views: 1,315
Posted By kumardeep
Query regarding the cuffdiff command to get differential gene expression

Hi
I am using RNA-seq data to use "Differential gene expression". For that I have taken data from SRA (NCBI) raw files of human sample in some experiment (Control- 3 files; each of size ~1GB and...
Forum: Bioinformatics 05-09-2012, 12:02 AM
Replies: 7
Views: 3,933
Posted By kumardeep
Hi all I have RNA-seq data (2 control sets and...

Hi all
I have RNA-seq data (2 control sets and 2 test sets). I have generated the *.sorted.bam files (~1GB) through bowtie software. Right now I am using cufflinks software to generate RPKM values...
Forum: Introductions 04-21-2012, 11:46 PM
Replies: 6
Views: 4,596
Posted By kumardeep
Thanks for the guidance. Sure, will go through...

Thanks for the guidance. Sure, will go through these links and see what I get ..........:)
Forum: Introductions 04-21-2012, 12:17 AM
Replies: 6
Views: 4,596
Posted By kumardeep
Hi I downloaded the hg19.2bit file from UCSC...

Hi
I downloaded the hg19.2bit file from UCSC browser site. Then converted that into fasta format using twoBitToFa utility. hg19.2bit was ~778 MB and hg19.fa was 3 GB. But when I opened that .fa file...
Forum: Introductions 04-20-2012, 10:40 PM
Replies: 6
Views: 4,596
Posted By kumardeep
Thanks for the suggestions.

Thanks for the suggestions.
Forum: Introductions 04-20-2012, 06:48 AM
Replies: 6
Views: 4,596
Posted By kumardeep
RNA-seq READS mapping on Reference Genome

Hi all
I am new entrant on this platform. I am a tyro on NGS analysis. What motivated me to come into this field is basically emergence of NGS data exponentially. Also presently my project is...
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