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Search: Posts Made By: oxydeepu
Forum: Literature Watch 03-14-2016, 12:18 PM
Replies: 41
Views: 28,317
Posted By oxydeepu
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...
Forum: Literature Watch 03-14-2016, 08:27 AM
Replies: 41
Views: 28,317
Posted By oxydeepu
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...
Forum: Literature Watch 03-14-2016, 02:01 AM
Replies: 41
Views: 28,317
Posted By oxydeepu
Thank you Eric. I will try and let you know. ...

Thank you Eric. I will try and let you know.

Best,
Deepak
Forum: Literature Watch 03-12-2016, 10:31 AM
Replies: 41
Views: 28,317
Posted By oxydeepu
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...
Forum: Literature Watch 03-11-2016, 11:28 AM
Replies: 41
Views: 28,317
Posted By oxydeepu
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...
Forum: Literature Watch 03-11-2016, 08:18 AM
Replies: 41
Views: 28,317
Posted By oxydeepu
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...
Forum: Literature Watch 03-10-2016, 07:39 AM
Replies: 41
Views: 28,317
Posted By oxydeepu
Hi Eric, I have solved the problems with the...

Hi Eric,

I have solved the problems with the reference. But now the problem seems to be different at the step of calculating coverage. This is the error I get.
...
Forum: Literature Watch 03-08-2016, 04:25 AM
Replies: 41
Views: 28,317
Posted By oxydeepu
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...
Forum: Bioinformatics 04-12-2013, 01:52 AM
Replies: 7
Views: 1,306
Posted By oxydeepu
So now I can include this gff also to the IGV...

So now I can include this gff also to the IGV viewer and visualise. So does this take care of the exon informations, any clue about that?

Thanks,
Deepak
Forum: Bioinformatics 04-12-2013, 01:41 AM
Replies: 7
Views: 1,306
Posted By oxydeepu
WHat about the second question?

WHat about the second question?
Forum: Bioinformatics 04-12-2013, 01:26 AM
Replies: 7
Views: 1,306
Posted By oxydeepu
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...
Forum: Bioinformatics 04-12-2013, 12:22 AM
Replies: 7
Views: 1,306
Posted By oxydeepu
Visualing the alignment on a genome without annotations

Hi All,

I'm working in a lab which uses planaria as a model organism, which have a contig level of genome assembly. I have RNA-Seq data from the same. Now I am trying to visualize the alignment of...
Forum: Bioinformatics 10-25-2012, 12:01 AM
Replies: 1
Views: 2,127
Posted By oxydeepu
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
Forum: Bioinformatics 08-09-2012, 12:41 AM
Replies: 5
Views: 4,971
Posted By oxydeepu
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...
Forum: Bioinformatics 07-04-2012, 10:33 AM
Replies: 13
Views: 5,923
Posted By oxydeepu
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...
Forum: Bioinformatics 05-25-2012, 01:53 AM
Replies: 1
Views: 2,323
Posted By oxydeepu
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...
Forum: Bioinformatics 05-02-2012, 01:14 AM
Replies: 3
Views: 1,908
Posted By oxydeepu
Thanks alot kopi-o.. I will try using them. ...

Thanks alot kopi-o..

I will try using them.

cheers
deepak
Forum: Bioinformatics 05-01-2012, 11:08 PM
Replies: 3
Views: 1,908
Posted By oxydeepu
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
Forum: Bioinformatics 04-30-2012, 12:48 AM
Replies: 0
Views: 1,098
Posted By oxydeepu
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...
Forum: Bioinformatics 04-24-2012, 11:43 PM
Replies: 4
Views: 1,767
Posted By oxydeepu
Thank you. Is there any other way we can...

Thank you.

Is there any other way we can figure out from the alignment output whether it is coming from an exonic region or repeat region.

Cheers
Deepak
Forum: Bioinformatics 04-24-2012, 09:44 PM
Replies: 4
Views: 1,767
Posted By oxydeepu
Sorry for incomplete question. I meant from the...

Sorry for incomplete question. I meant from the bowtie output file.

Deepak
Forum: Bioinformatics 04-24-2012, 09:51 AM
Replies: 4
Views: 1,767
Posted By oxydeepu
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...
Forum: Bioinformatics 04-03-2012, 11:35 PM
Replies: 6
Views: 2,414
Posted By oxydeepu
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...
Forum: Bioinformatics 04-01-2012, 11:19 PM
Replies: 1
Views: 1,492
Posted By oxydeepu
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...
Forum: Bioinformatics 03-20-2012, 10:08 PM
Replies: 4
Views: 1,882
Posted By oxydeepu
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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