Forum: Bioinformatics
05-15-2013, 03:51 PM
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Replies: 1
Views: 1,755
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Forum: Bioinformatics
03-17-2012, 05:22 PM
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Replies: 12
Views: 4,663
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Forum: Bioinformatics
03-17-2012, 02:17 PM
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Replies: 2
Views: 6,228
unmapped vs soft-clipping
quite confused about this two terminology. I'm reading Pindel, the split-read algorithm. The author seems to make use of the information of "unmapped" reads. Also there are other split-read-based...
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Forum: Bioinformatics
03-17-2012, 01:41 PM
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Replies: 11
Views: 15,537
This may be a late answer.
To my...
This may be a late answer.
To my understanding, you guys are confused about "-q opiton(quality trimming)" and " soft-clipped".
-q option is to trim those crappy ends of reads with very low...
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Forum: Bioinformatics
03-17-2012, 11:06 AM
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Replies: 12
Views: 4,663
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Forum: Bioinformatics
03-09-2012, 08:11 AM
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Replies: 12
Views: 4,663
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Forum: Bioinformatics
01-29-2012, 06:28 AM
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Replies: 6
Views: 2,122
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Forum: Bioinformatics
11-27-2011, 05:52 PM
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Replies: 1
Views: 1,836
BWA trim doesn’t work.
I tried to run BWA with trimming those low-quality bases around the end of read. And command is like:
/share/bin/bwa aln -t 7 -I -q 20 ****.txt.gz > ****.sai
Here -I is to convert Illumina...
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Forum: Bioinformatics
11-19-2011, 04:39 PM
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Replies: 1
Views: 2,664
Pindel problem
I downloaded the binary code of latest version of Pindel.
And then run the command like below;
./pindel_x86_64 -f /home/xxx/data/human_g1k_v37.fasta -i /home/xxx/scratch/S00005/config.txt -c ALL...
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Forum: Bioinformatics
10-21-2011, 07:07 AM
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Replies: 39
Views: 15,610
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Forum: Bioinformatics
09-14-2011, 10:03 AM
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Replies: 0
Views: 1,743
Variation-Hunter empty output
I don't know if anyone here has used Variation-Hunter.
I used the *.vh files generated from mrFAST as the input of Variation-Hunter.
But it seems I only get empty output.
15M...
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Forum: Bioinformatics
07-07-2011, 01:15 PM
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Replies: 0
Views: 2,335
CNVnator make histogram problem
I'm doing trio data analysis; so I merged those small root files into larger ones chromosome by chromosome. The merge process looks ok.
But when I tried to make histogram out of it, I got errors...
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Forum: Bioinformatics
07-05-2011, 09:07 AM
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Replies: 2
Views: 2,623
CNV core dump problem
HI I'm using CNVnator to do some CNV analysis but came across problems of core dump
Basically I first generated .root files from .bam files; then merged those small .root files into larger ones....
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Forum: Bioinformatics
06-27-2011, 04:03 PM
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Replies: 0
Views: 1,545
Save error report as text file in BWA
Hi I'm using SUN Grid Engine to submit BWA jobs, written by shell script like this:
#!/bin/bash
#$ -pe single 24
#$ -V
#$ -cwd
#$ -o $HOME/sge_jobs_output/sge_job.$JOB_ID.out -j y
#$ -S...
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Forum: Bioinformatics
06-22-2011, 06:13 AM
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Replies: 5
Views: 2,217
THanks everyone.
I think the core question...
THanks everyone.
I think the core question is: how can we guarantee the quality of the generated .sai, .sam file? How do you know the programming at this step is complete? Just look at the size of...
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Forum: Bioinformatics
06-21-2011, 04:13 PM
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Replies: 5
Views: 2,217
About script to combine steps of BWA
For BWA, first do alignment (generate .sai), then sampe the paired-ends (generate .sam), then convert .sam to .bam. Now I'm going to write script to combine all these steps. ie, input is fastq, then...
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Forum: Bioinformatics
06-16-2011, 07:33 PM
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Replies: 1
Views: 2,184
BWA weird thing
HI guys
I ran programs to generate .sam files, but find some weird things.
432M ERR001275_1.recal.fastq.gz
432M ERR001275_1.sai
434M ERR001275_2.recal.fastq.gz
437M ERR001275_2.sai
8.0K...
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Forum: Bioinformatics
06-16-2011, 06:58 AM
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Replies: 39
Views: 15,610
Thx Prakhar,
Sorry for my delayed response....
Thx Prakhar,
Sorry for my delayed response. The problem of viewing has been solved. Yeah, you are right, use ssh -X and it works! thx~
I'm actually now trying larger-scale data on cluster, and...
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Forum: Bioinformatics
06-15-2011, 12:56 PM
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Replies: 1
Views: 2,658
Confused about .sai file size
Yesterday I ran hundreds, if not thousands of alignment of fastq files to human genome, so I have some findings. Just look at below:
1.3G SRR010942_2.recal.fastq.gz
259M SRR010942_2.sai...
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Forum: Bioinformatics
06-14-2011, 05:40 PM
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Replies: 5
Views: 3,447
Many many thanks Kennels!!!
Yeah, I just...
Many many thanks Kennels!!!
Yeah, I just made the spreadsheet, actually with 800 fastq files. And the shell script works quite well!
btw, can you give any clue about writing Perl to finish such...
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Forum: Bioinformatics
06-14-2011, 04:02 PM
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Replies: 5
Views: 3,447
Run hundreds of BWA commands without waiting
Hi guys
I'm analyzing some high-coverage trio data. So Need to run BWA for hundreds of fastq.gz files. Obviously I should write some script to finish such task without waiting and typing in hundreds...
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Forum: Bioinformatics
06-14-2011, 06:38 AM
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Replies: 39
Views: 15,610
thx guys.
I tried using ssh -X, but still...
thx guys.
I tried using ssh -X, but still doesn't work.
[xug@pem610-006 src]$ ./cnvnator -root NA18507.root -view 100
>chr12 11396601 11436500
>
I can see nothing except the new prompt.
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Forum: Bioinformatics
06-13-2011, 08:54 PM
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Replies: 39
Views: 15,610
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Forum: Bioinformatics
06-13-2011, 03:35 PM
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Replies: 39
Views: 15,610
Just now I tried the whole genome (no longer...
Just now I tried the whole genome (no longer specific to chr1): ./cnvnator -root NA18507. root -tree ***.bam
Then it pop out:
Out of bound coordinate 199501844 for chromosome 'chr3'.
Out of...
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Forum: Bioinformatics
06-13-2011, 03:21 PM
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Replies: 39
Views: 15,610
thx Michael.
Now I've gone through the...
thx Michael.
Now I've gone through the whole steps of CNVnator and seems quite good. The only problem now is at the final step about visualizing the CNV. I enter a genomic region at the prompt...
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