Forum: Literature Watch
03-14-2016, 12:18 PM
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Replies: 41
Views: 28,845
Hi Eric,
Sorry to flood you with questions....
Hi Eric,
Sorry to flood you with questions. one more thing, my files have same naming for normals across samples and it is giving me an error saying Dupicate ID. The problem is the files are write...
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Forum: Literature Watch
03-14-2016, 08:27 AM
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Replies: 41
Views: 28,845
Dear Eric,
CNVkit worked when I used the...
Dear Eric,
CNVkit worked when I used the older version of pysam. Now I have a doubt regarding running CNVkit. I have 20 samples with matched tumor and normal. Do I make reference from all normal...
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Forum: Literature Watch
03-14-2016, 02:01 AM
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Replies: 41
Views: 28,845
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Forum: Literature Watch
03-12-2016, 10:31 AM
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Replies: 41
Views: 28,845
Dear Eric,
I tried all possible removal...
Dear Eric,
I tried all possible removal of chr as my BAM file is with just chromosome numbers.But still ended up getting same error as I mentioned above. Now the target and the anti target files...
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Forum: Literature Watch
03-11-2016, 11:28 AM
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Replies: 41
Views: 28,845
Hi Eric,
Thanks for the reply. I cross...
Hi Eric,
Thanks for the reply. I cross checked chr notations in bam and reference bed file. It is all without chr. But when it creates antitarget files it adds chr to the file and vice versa if I...
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Forum: Literature Watch
03-11-2016, 08:18 AM
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Replies: 41
Views: 28,845
Dear Eric,
Thank you for sparing your time....
Dear Eric,
Thank you for sparing your time. I tried the target and it gives a 4 field bed. But I gues the problem is coming when I use the BAM files.
###################
cnvkit.py batch...
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Forum: Literature Watch
03-10-2016, 07:39 AM
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Replies: 41
Views: 28,845
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Forum: Literature Watch
03-08-2016, 04:25 AM
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Replies: 41
Views: 28,845
Sequence IDs don't match with bed Error CNVkit.
Hi all,
I trying to run CNVkit with tumor and normal samples on exome sequencing. But I tried all possible things mentioned in the docs. I tried different bed file input as the target region and...
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Forum: Bioinformatics
04-12-2013, 01:52 AM
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Replies: 7
Views: 1,338
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Forum: Bioinformatics
04-12-2013, 01:41 AM
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Replies: 7
Views: 1,338
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Forum: Bioinformatics
04-12-2013, 01:26 AM
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Replies: 7
Views: 1,338
Thank You Nico,
I will definitely try the...
Thank You Nico,
I will definitely try the suggestion. One doubt, does IGV, inputs a genome fasta file or does it have a built in database for genomes? What If I want to put in the EST alignment...
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Forum: Bioinformatics
04-12-2013, 12:22 AM
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Replies: 7
Views: 1,338
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Forum: Bioinformatics
10-25-2012, 12:01 AM
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Replies: 1
Views: 2,161
Problem with GenScan.
I Have similiar problem with the genscan predictions. I have an extra doubt, does it give you the 3' UTR of the gene prediction?
Thank you in advance,
Best Regards,
Deepak
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Forum: Bioinformatics
08-09-2012, 12:41 AM
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Replies: 5
Views: 5,004
Hi all,
I have question on how to plot...
Hi all,
I have question on how to plot wiggle tracks. I just have a wig file and a reference genome fasta. Can anyone suggest me some ways i can plot the wiggle into a nice figure.
Thanks in...
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Forum: Bioinformatics
07-04-2012, 10:33 AM
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Replies: 13
Views: 5,948
Hi all,
Am following the guide lines...
Hi all,
Am following the guide lines mentioned in the scripture walk through example.
But the command
java -Xmx4000m -jar scripture.jar -task makePairedFile -pair1...
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Forum: Bioinformatics
05-25-2012, 01:53 AM
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Replies: 1
Views: 2,355
GTF file for reference of human transcriptome
Hi all,
I have the human transcriptome downloaded from unigene. Is there any other resources where you can get the human transcriptome.? I have the fasta file of the transcriptome. how can i make...
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Forum: Bioinformatics
05-02-2012, 01:14 AM
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Replies: 3
Views: 1,929
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Forum: Bioinformatics
05-01-2012, 11:08 PM
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Replies: 3
Views: 1,929
ChIP-Seq Peak Calling tools
Hi all,
Is there any tools to study the ChIP-Seq peak calling tools which can be used without a control sample.
Thank you
cheers
deepak
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Forum: Bioinformatics
04-30-2012, 12:48 AM
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Replies: 0
Views: 1,127
How To make mapping density of bowtie alignments
Hi all,
I have aligned the RNA-Seq reads generated in the lab to the transcriptome available using bowtie1. I want to make the wiggle tracks or mapping density of the reads to each contig. So that...
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Forum: Bioinformatics
04-24-2012, 11:43 PM
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Replies: 4
Views: 1,789
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Forum: Bioinformatics
04-24-2012, 09:44 PM
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Replies: 4
Views: 1,789
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Forum: Bioinformatics
04-24-2012, 09:51 AM
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Replies: 4
Views: 1,789
Bowtie alignment distribution
hi all,
I have aligned my RNA-Seq reads to the reference genome using bowtie. Now i want to know where the reads are getting aligned from the map file - like is it coming from repetitive element...
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Forum: Bioinformatics
04-03-2012, 11:35 PM
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Replies: 6
Views: 2,441
Similiar sort of problem.
Hi all,
I am getting this error
Traceback (most recent call last):
File "/home/deepak/bioTools/tophat-1.3.1.Linux_x86_64//tophat", line 2607, in ?
sys.exit(main())
File...
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Forum: Bioinformatics
04-01-2012, 11:19 PM
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Replies: 1
Views: 1,520
Tophat for multiple files.
Hi all,
I have three fastq file for a sample. two paired end reads and a single - end read for the same.
I want to run tophat for all together. i want to know is it possible to run 3 fq files...
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Forum: Bioinformatics
03-20-2012, 10:08 PM
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Replies: 4
Views: 1,912
Hi,
@Kaustubh: i have done the same as you...
Hi,
@Kaustubh: i have done the same as you suggested. i just want an assurance that it will work fine.
@pbluescript: No i havent tried cuffmerge. Can you please help me how to do it..??
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