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Search: Posts Made By: jlfmssm
Forum: Bioinformatics 07-15-2010, 07:38 AM
Replies: 0
Views: 1,194
Posted By jlfmssm
Smile cuffdiff question

I am trying to run cuffdiff like the following:

/cluster2/aimin/cufflinks-0.8.3-1309/bin/cuffdiff -m 50 /cluster2/aimin/MGED_13/ensemble_snippet.gtf...
Forum: RNA Sequencing 07-15-2010, 07:34 AM
Replies: 0
Views: 1,820
Posted By jlfmssm
Smile question about cuffdiff

I am trying to run cuffdiff like the following:

/cluster2/aimin/cufflinks-0.8.3-1309/bin/cuffdiff -m 50 /cluster2/aimin/MGED_13/ensemble_snippet.gtf...
Forum: Bioinformatics 07-05-2010, 07:19 PM
Replies: 6
Views: 3,611
Posted By jlfmssm
[QUOTE=jlfmssm;21354]Yes, here is A.bed: ...

[QUOTE=jlfmssm;21354]Yes, here is A.bed:

chr6_cox_hap1 2140627 2140761 IL26_1382:1:6:405:885 0 +
chr8 74366566 74366678 IL26_1382:1:6:406:42 0 +
chr11 ...
Forum: Bioinformatics 07-05-2010, 07:17 PM
Replies: 6
Views: 3,611
Posted By jlfmssm
Yes, here is A.bed: chr6_cox_hap1 2140627...

Yes, here is A.bed:

chr6_cox_hap1 2140627 2140761 IL26_1382:1:6:405:885 0 +
chr8 74366566 74366678 IL26_1382:1:6:406:42 0 +
chr11 10831430 10831500 ...
Forum: Bioinformatics 07-05-2010, 05:15 PM
Replies: 6
Views: 3,611
Posted By jlfmssm
Smile thanks, As you said, but I got this error: ...

thanks,

As you said, but I got this error:
Error: malformed BED entry at line 41767. Coordinate detected that is < 0. Exiting.
Forum: Bioinformatics 07-05-2010, 02:55 PM
Replies: 6
Views: 3,611
Posted By jlfmssm
Smile queston for count of properly-paired end

I am using samtools and bamToBed to get the properly-paired read like this:

samtools view -bf 0x2 read.bam | bamToBed -i stdin > A.bed

then I use coverageBed to get counts for eahc gene in hg18...
Forum: Bioinformatics 06-28-2010, 09:11 PM
Replies: 2
Views: 4,171
Posted By jlfmssm
Smile coverageBed question

I try to run coverageBed like this:
/home/ay55/BEDTools/bin/genomeCoverageBed -ibam 1382_1_sorted.bam -i hg18.bed.sorted -g hg18.genome > hg18_seq.cov.txt

no error at all, but when I open...
Forum: Bioinformatics 06-28-2010, 09:09 PM
Replies: 46
Views: 29,403
Posted By jlfmssm
Smile coverageBed question

I try to run coverageBed like this:
/home/ay55/BEDTools/bin/genomeCoverageBed -ibam 1382_1_sorted.bam -i hg18.bed.sorted -g hg18.genome > hg18_seq.cov.txt

no error at all, but when I open...
Forum: Bioinformatics 06-27-2010, 04:35 PM
Replies: 0
Views: 1,342
Posted By jlfmssm
Smile time issue for bwa

I am trying to use bwa to perform alignment like the following:


#!/bin/sh
#PBS -S /bin/sh
#PBS -N run_aln
#PBS -m abe
#PBS -r n
#PBS -l walltime=100:00:00
#PBS -l mem=4GB
Forum: Bioinformatics 06-26-2010, 07:32 AM
Replies: 1
Views: 1,832
Posted By jlfmssm
question about bwa

I tried to run bwa as the following:
/usr/local/bin/bwa index -p /cluster2/aimin/data_from_nature_publication/Reference/hg19 /cluster2/aimin/data_from_nature_publication/Reference/hg19.fa

However...
Forum: Bioinformatics 06-25-2010, 07:13 PM
Replies: 5
Views: 5,576
Posted By jlfmssm
but I got this: [aimin@node01 all_sam_data]$...

but I got this:
[aimin@node01 all_sam_data]$ samtools view -S -X 1382_1.sam/1382_1.sam -o 1382_1_test.out
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!
What I should do...
Forum: Bioinformatics 06-25-2010, 04:41 PM
Replies: 5
Views: 5,576
Posted By jlfmssm
Thanks, I tried, but I got this error: ...

Thanks, I tried, but I got this error:

[aimin@node01 all_sam_data]$ samtools view -X 1382_1.sam/1382_1.sam
[bam_header_read] EOF marker is absent.
[main_samview] fail to read the header.
Forum: Bioinformatics 06-25-2010, 03:07 PM
Replies: 5
Views: 5,576
Posted By jlfmssm
Smile How to check read are properly paired from SAM file?

I am new for NGS data.
How to check reads are properly paired from SAM file?
It is appreciated someone can point me some programs?

Thanks,
Aimin
Forum: Introductions 04-23-2010, 03:31 PM
Replies: 0
Views: 1,006
Posted By jlfmssm
Post Hello to all

I am new to next generation sequence data analysis,so if I asked naive question, please don't laugh at me.

Thanks,

jlf
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