Forum: Bioinformatics
07-15-2010, 08:38 AM
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Replies: 0
Views: 1,258
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...
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Forum: RNA Sequencing
07-15-2010, 08:34 AM
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Replies: 0
Views: 1,888
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...
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Forum: Bioinformatics
07-05-2010, 08:19 PM
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Replies: 6
Views: 3,721
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Forum: Bioinformatics
07-05-2010, 08:17 PM
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Replies: 6
Views: 3,721
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Forum: Bioinformatics
07-05-2010, 06:15 PM
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Replies: 6
Views: 3,721
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Forum: Bioinformatics
07-05-2010, 03:55 PM
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Replies: 6
Views: 3,721
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...
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Forum: Bioinformatics
06-28-2010, 10:11 PM
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Replies: 2
Views: 4,237
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...
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Forum: Bioinformatics
06-28-2010, 10:09 PM
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Replies: 46
Views: 29,928
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...
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Forum: Bioinformatics
06-27-2010, 05:35 PM
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Replies: 0
Views: 1,398
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
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Forum: Bioinformatics
06-26-2010, 08:32 AM
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Replies: 1
Views: 1,883
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...
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Forum: Bioinformatics
06-25-2010, 08:13 PM
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Replies: 5
Views: 5,770
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...
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Forum: Bioinformatics
06-25-2010, 05:41 PM
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Replies: 5
Views: 5,770
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.
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Forum: Bioinformatics
06-25-2010, 04:07 PM
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Replies: 5
Views: 5,770
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Forum: Introductions
04-23-2010, 04:31 PM
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Replies: 0
Views: 1,035
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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