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Forum: Bioinformatics 05-28-2013, 06:55 AM
Replies: 2
Views: 2,418
Posted By wangli
It works when removing -R flag. Thank you, win804!

It works when removing -R flag. Thank you, win804!
Forum: Bioinformatics 05-26-2013, 05:03 PM
Replies: 2
Views: 2,418
Posted By wangli
samtools mpileup error

samtools mpileup -C50 -I -ugf -R myReference.fa myInput.bam | bcftools view -bvcg - > samtoolsSNPs.raw.bcf

[fai_load] build FASTA index.
open: No such file or directory
[_razf_open] fail to open...
Forum: Bioinformatics 05-21-2013, 02:15 PM
Replies: 24
Views: 21,262
Posted By wangli
Is anyone still interested in this question? I...

Is anyone still interested in this question? I recently noticed the consequence of using the lenient stringency in Picard. When AddOrReplace read groups, the strict mode will generate some column...
Forum: Bioinformatics 05-21-2013, 01:51 PM
Replies: 17
Views: 46,468
Posted By wangli
Could you please further specify how to fix the...

Could you please further specify how to fix the .bam file? I donot want to use the lenient stringency in Picard, because it causes my further problem when calling SNPs in GATK.
Forum: RNA Sequencing 11-02-2012, 09:06 AM
Replies: 3
Views: 3,166
Posted By wangli
how to calculate the mean sequencing depth of RNA-seq

Dear users

I tried to calculate the mean sequencing depth of RNA-seq. Firstly, I utilized GATK to calculate that with the whole genome as reference. It turned out that some samples with around 15...
Forum: Bioinformatics 07-13-2012, 10:41 AM
Replies: 21
Views: 20,647
Posted By wangli
I also had the problem when using nohup. Without...

I also had the problem when using nohup. Without nohup. it goes well.
Forum: Bioinformatics 07-12-2012, 10:19 AM
Replies: 0
Views: 1,724
Posted By wangli
how to account for the output of DepthOfCoverage in GATK

Hi, all

I want to check the mean depth of coverage of my bam file. The following is the content of the output file coverage.out.sample_summary:
sample_id total mean granular_third_quartile...
Forum: Bioinformatics 07-09-2012, 10:10 AM
Replies: 5
Views: 7,374
Posted By wangli
Hi, Andreas I would like to thank you for...

Hi, Andreas

I would like to thank you for your very useful information here. I got my similar problem fixed according to your suggestions.
Actually, I have used the same dictionary for other...
Forum: Bioinformatics 07-02-2012, 10:51 AM
Replies: 0
Views: 702
Posted By wangli
GATK sequencing reads file

Dear All

I am trying to use GATK for multiple samples SNP calling. The requirement of input sequence reads file of GATK is 1) .bam 2) indexed 3) coordinate sorted 4) with read group including PL...
Forum: Bioinformatics 06-29-2012, 10:15 AM
Replies: 0
Views: 1,657
Posted By wangli
gene ID type

Dear All

I am using DAVID to do the pathway and GO analysis. My selected differentially expressed gene IDs are as follows: POPTR_0002s23610, PopTR_0014s19710, which are from the Populus...
Forum: RNA Sequencing 06-09-2012, 02:55 PM
Replies: 4
Views: 18,503
Posted By wangli
Thanks a lot, dpryan! It works!

Thanks a lot, dpryan! It works!
Forum: RNA Sequencing 06-09-2012, 10:08 AM
Replies: 4
Views: 18,503
Posted By wangli
Thanks, dpryan! I made a file named as...

Thanks, dpryan!

I made a file named as htseq_count.py and then execute it in the terminal.

The content of the file is as follows:
#!/usr/bin/python2.6 -tt

import numpy
import HTSeq
Forum: RNA Sequencing 06-08-2012, 04:35 PM
Replies: 5
Views: 3,786
Posted By wangli
you can look into the following thread: ...

you can look into the following thread:
http://seqanswers.com/forums/showthread.php?t=15092
Forum: RNA Sequencing 06-08-2012, 03:52 PM
Replies: 5
Views: 3,786
Posted By wangli
Hi, gtf_to_sam should be specified in your PATH. ...

Hi, gtf_to_sam should be specified in your PATH.
You need to type the following command in your terminal:
PATH=$PATH:/PATH/TO/gtf_to_sam
Forum: RNA Sequencing 06-08-2012, 03:10 PM
Replies: 4
Views: 18,503
Posted By wangli
HTSeq errors

Hi, dear patrons

i had an error when running HT-seq in python.

******$ python
Python 2.6.1 (r261:67515, Aug 2 2010, 20:10:18)
[GCC 4.2.1 (Apple Inc. build 5646)] on darwin
Type "help",...
Forum: RNA Sequencing 06-07-2012, 02:04 PM
Replies: 8
Views: 2,210
Posted By wangli
Hi, Adameur Thanks for your information....

Hi, Adameur

Thanks for your information. Could you please provide further information concerning how to distinguish nascent transcripts from true novel genes?

Thanks
Forum: Bioinformatics 06-07-2012, 10:04 AM
Replies: 4
Views: 5,730
Posted By wangli
I tried to install HTseq 0.5.3 source package,...

I tried to install HTseq 0.5.3 source package, but Xcode is not installed on my computer, and I cannot get it installed now. Do anyone know where i can get the binary package of HTseq, which doesnot...
Forum: RNA Sequencing 06-07-2012, 09:32 AM
Replies: 8
Views: 2,210
Posted By wangli
In my experience, "cuffmerge" and "cuffdiff"...

In my experience, "cuffmerge" and "cuffdiff" detect around 4000 novel genes, which represents 10% of the total gene, which seems totally out of our expectation and might be far from the truth. So, it...
Forum: RNA Sequencing 06-06-2012, 04:11 PM
Replies: 8
Views: 2,210
Posted By wangli
I am kind of on the same boat. As far as i know,...

I am kind of on the same boat. As far as i know, the tophat/cufflinks pipeline can detect some novel genes compared to the reference genome. If I am interested if those novel gene are differentially...
Forum: RNA Sequencing 06-04-2012, 10:39 AM
Replies: 61
Views: 35,784
Posted By wangli
error in cummeRbund

Hi, I found the post is very helpful. I am struggling with cummeRbund now. I tried some codes listed here, and am confronted with some errors.

> cuff_data <- readCufflinks('diff_out')
>...
Forum: RNA Sequencing 06-03-2012, 04:54 PM
Replies: 16
Views: 5,399
Posted By wangli
Maybe the new version is not stable. I utilized V...

Maybe the new version is not stable. I utilized V 2.0.0, it works well. You can write to the following email to report the error and for suggestions: tophat.cufflinks@gmail.com
Forum: Bioinformatics 05-30-2012, 07:10 AM
Replies: 23
Views: 16,468
Posted By wangli
Dear cewells I defined the path in the...

Dear cewells

I defined the path in the command line.
But when I utilized .~/.bashrc, it showed that it cannot find the file or directory.
I used ls -a to see the hidden file, but no .bashrc....
Forum: RNA Sequencing 05-30-2012, 06:56 AM
Replies: 5
Views: 3,786
Posted By wangli
cuffmerge error

Hi, I am confronted with some errors when doing cuffmerge analysis.

/home/bin/cuffmerge -g Ptrichocarpa_156_gene.gff3 -s Ptrichocarpa_156_hardmasked.fa -p 10 assemblies.txt

[Wed May 30 09:48:20...
Forum: RNA Sequencing 05-29-2012, 11:41 AM
Replies: 16
Views: 5,399
Posted By wangli
Currently, I am working with v 2.0.0, which works...

Currently, I am working with v 2.0.0, which works well.
From your error, it seems that your sequences are paired-end. In this case, -r flag is required.
Forum: RNA Sequencing 05-24-2012, 10:31 AM
Replies: 16
Views: 5,399
Posted By wangli
The v.2.0.2 has been released recently. But the...

The v.2.0.2 has been released recently. But the author said it is not totally ready to go. He still suggested to use v.2.0.0.
You can contact the above-mentioned email address....
Showing results 1 to 25 of 48

 


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