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Search: Posts Made By: rahilsethi
Forum: Bioinformatics 07-06-2018, 10:21 AM
Replies: 0
Views: 640
Posted By rahilsethi
ViralFusionSeq not finding human-virus fusion regions

I ran ViralFusionSeq, first on test dataset, given with the software package. I took one the contig assembly sequence generated by tool in the final contig output file. The contig sequence showed...
Forum: Bioinformatics 03-09-2015, 04:16 AM
Replies: 2
Views: 2,596
Posted By rahilsethi
Multiple entries of a gene/locus at Cuffdiff Differential Gene Expression Output

Hi,

I'm also getting this probelm (gene_exp.diff):

XLOC_021564 Hnf4a 3:165976692-166162683
XLOC_022796 Hnf4a 3:165976692-166162683
XLOC_022797 Hnf4a 3:165976692-166162683

When I looked at...
Forum: Bioinformatics 05-23-2013, 05:58 AM
Replies: 2
Views: 5,131
Posted By rahilsethi
NH:i:1 does not give uniquely mapped reads when TopHat run under default settings

No, when running TopHat "NH:i:1" will not report uniquely mapped reads when run with default settings. This is because under default settings max no of reported primary alignments are 20 even when it...
Forum: Bioinformatics 10-22-2012, 10:20 AM
Replies: 15
Views: 7,272
Posted By rahilsethi
I did not use bwa. I used SHRiMP 2.2.2 for...

I did not use bwa. I used SHRiMP 2.2.2 for mapping. samtools 1.8 for converting sam to bam and Picard version: 1.74 for combining mapped bam files.
Forum: Bioinformatics 10-10-2012, 11:25 AM
Replies: 5
Views: 4,129
Posted By rahilsethi
to add to the above a) my bam files are...

to add to the above
a) my bam files are generated by the same samtools version as the merged file and also for the sort and depth activities (0.1.18)
b) my bam files are also not truncated since...
Forum: Bioinformatics 10-10-2012, 11:21 AM
Replies: 5
Views: 4,129
Posted By rahilsethi
Question samtools merge problem

Hi,

I am having the same problem as blair had when used samtools merge:

[bam_header_read] EOF marker is absent. The input is probably truncated.

I also followed the same steps

1. Files:...
Forum: Bioinformatics 10-10-2012, 05:05 AM
Replies: 2
Views: 1,483
Posted By rahilsethi
Hi nilshomer, Thanks for the suggestion....

Hi nilshomer,

Thanks for the suggestion. Although SHRiMP, in general, does not give any separate option for .qual files in the run, I did try to incorporate qual files along with csfasta; but it...
Forum: Bioinformatics 10-09-2012, 10:08 AM
Replies: 2
Views: 1,483
Posted By rahilsethi
Unhappy SHRiMP 2 output problem

Hi,

I used SHRiMP 2.2.2 for mapping (gapped mapping) SOLiD Paired End data to hg19 genome reference. The SAM output file does not have any value at QV column, instead has "*" as a placeholder. For...
Forum: Bioinformatics 10-04-2012, 01:14 PM
Replies: 15
Views: 7,272
Posted By rahilsethi
Unhappy Picard java exception

Hi I got similar error using Picard MergeSamFiles.jar
Wondering if anyone found an answer for it

Exception in thread "main" net.sf.samtools.util.RuntimeIOException:...
Forum: Bioinformatics 09-19-2012, 08:36 AM
Replies: 1
Views: 841
Posted By rahilsethi
The version of SNVer I used here is 0.4.1

The version of SNVer I used here is 0.4.1
Forum: Bioinformatics 09-19-2012, 08:33 AM
Replies: 1
Views: 841
Posted By rahilsethi
SNVer Qval missing

Hi,

I used the following SNVer command for printing out putative variants in VCF format:

java -Xmx4g -jar ~/SNVer-0_4_1/SNVerIndividual.jar \
-i bamfile.bam \
-r hg19_ucsc.fasta \
-o...
Forum: Bioinformatics 09-14-2012, 12:02 PM
Replies: 4
Views: 1,332
Posted By rahilsethi
Unhappy SHRiMP2 slow for higher organisms

I tried to run SHRiMP2 once on SOLiD paired end ChipSeq data with mouse genome as reference and it never finished running despite giving a threading option. Now with gapped alignment (to obtain...
Forum: Bioinformatics 09-07-2012, 07:01 AM
Replies: 138
Views: 64,817
Posted By rahilsethi
Question GATK -dcov option???

I have additional question to raonyguimaraes's post
Does anyone know in details about GATK -dcov option in UnifiedGenotyper. I tried to look in GATK Manual but could not find much about it other...
Forum: Bioinformatics 10-12-2011, 09:15 AM
Replies: 513
Views: 199,869
Posted By rahilsethi
Re: Extra parameter(s) specified error

the reason why I did not give any value to -n and --maxbts because I am trying to use their default values. If I wouldn't mention -n then how would bowtie know whether I want to do mapping with -n or...
Forum: Bioinformatics 10-12-2011, 05:20 AM
Replies: 513
Views: 199,869
Posted By rahilsethi
Unhappy Extra parameter(s) specified error

I am running bowtie version 0.12.7 for mapping SOLiD (colorspace 50bp read length) data against human genome (hg19), on a linux platform (CentOS). When I run with the following parameters:



it...
Forum: Bioinformatics 10-07-2011, 10:38 AM
Replies: 1
Views: 3,721
Posted By rahilsethi
Unhappy Extra parameter(s) specified error

I too have been getting the same error
I am running bowtie version 0.12.7 for mapping SOLiD (colorspace 50bp read length) data
against human genome (hg19), on a linux platform (CentOS). When I run...
Forum: SOLiD 11-15-2010, 06:55 AM
Replies: 6
Views: 2,828
Posted By rahilsethi
Question Total Mapped region of reference?

Hi everyone,

I'm sorry for the deviation from the main question of this thread. Since I was not able to find how to start a new thread, this was the thread that I could find that is related most...
Forum: SOLiD 09-09-2010, 12:06 PM
Replies: 3
Views: 2,231
Posted By rahilsethi
What it has to do with my analysis? The result is...

What it has to do with my analysis? The result is straight from the software SOLiD SAGE Analysis tool. In the result.tab file it produces read ids for the tags are mentioned. I counted the unique set...
Forum: SOLiD 09-09-2010, 11:04 AM
Replies: 0
Views: 1,696
Posted By rahilsethi
Post SOLiD SAGE: low percentage of reads mapped

Hello,

I was analyzing the SOLiD SAGE data of human sequence using SOLiD SAGE Analysis tool. I performed Mapping using 27 bp length with 1 mismatch. The reference was the complete set of human...
Forum: SOLiD 09-09-2010, 10:41 AM
Replies: 3
Views: 2,231
Posted By rahilsethi
Post low percentage of reads mapped

Hello,

I was analyzing the SOLiD SAGE data of human sequence using SOLiD SAGE Analysis tool. I performed Mapping using 27 bp length with 1 mismatch. The reference was the complete set of human...
Forum: SOLiD 07-15-2010, 06:26 AM
Replies: 19
Views: 5,225
Posted By rahilsethi
How to find Percentage of reads mapped to reference???

how do I find out percentage of reads mapped to the
reference from SOLiD SAGE Analysis tool? In the mapping result, SOLiD SAGE
Analysis tool gives you the list of each type of tag and its count in...
Forum: SOLiD 05-13-2010, 11:26 AM
Replies: 19
Views: 5,225
Posted By rahilsethi
Post SOLiD SAGE Analysis software settings

I'm confused in selecting the option for the tag length and no of mismatches. I assume the tag length that has most no. of matches with the read can be determinant of which tag length is appropriate....
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