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Forum: Bioinformatics 05-07-2013, 06:35 AM
Replies: 6
Views: 6,252
Posted By alexbmp
I had the same error when running tophat for my...

I had the same error when running tophat for my fastq files.
I fixed this error; it happened only when my input fastq files were empty.

An index error occurs in

only because self.lastline is...
Forum: Bioinformatics 03-20-2012, 08:34 AM
Replies: 5
Views: 6,010
Posted By alexbmp
I haven't used NovoAlign, so don't fully trust me...

I haven't used NovoAlign, so don't fully trust me ;)

1-1. If you build alignment index before alignment, check if your index is in chromosomal order (chr1, chr2, chr3, ..., chrX, chrY, chrM or the...
Forum: Bioinformatics 03-20-2012, 02:37 AM
Replies: 5
Views: 6,010
Posted By alexbmp
If you are planning to use the Broad bundle, I...

If you are planning to use the Broad bundle,
I reckon the bundle for hg19 is present.

1. Have you tried downloading from the following ftp yet?...
Forum: Bioinformatics 03-19-2012, 07:41 PM
Replies: 0
Views: 1,502
Posted By alexbmp
Smile Questions about pathway analyses of genes with somatic mutations

Hi all :) !!

I sequenced cancer exomes matched with normal exomes, then after alignment follwed by de-duplication, I extracted significant somatic mutations from the pile-up files with VarScan...
Forum: Bioinformatics 02-12-2012, 11:03 PM
Replies: 7
Views: 4,784
Posted By alexbmp
Questions about VarScan

Hi all. I'm a student working to identify tumor-specific mutations.

Recently I've came up to VarScan and SomaticSniper.

There are some confusions about using VarScan, and I see that the...
Forum: Bioinformatics 02-11-2012, 12:58 AM
Replies: 13
Views: 7,585
Posted By alexbmp
Sorry for this late reply. Actually I didn't...

Sorry for this late reply.
Actually I didn't download NCBI dbsnp in VCF format;
I got it from the Broad Institute ftp ad dbsnp_132.hg19 in VCF format.

go to wget...
Forum: Bioinformatics 02-10-2012, 05:04 PM
Replies: 13
Views: 7,585
Posted By alexbmp
Thanks all. Actually I have downloaded dbSNP in...

Thanks all. Actually I have downloaded dbSNP in vcf from another site.
I still have not found any tool to convert flat dbSNP to VCF.
By the way, this liftOver tool Bukowski mentioned seems to be a...
Forum: Bioinformatics 12-27-2011, 10:09 PM
Replies: 0
Views: 1,287
Posted By alexbmp
Question Strange bug(?) in GATK

Just to see if anybody knows...

I got this funny error(?).

I ran GATK for chr1 (with -L chr1_startend.bed) for all of my reads in bam file,

then I ran GATK for hg18.fa (with no -L option)...
Forum: Bioinformatics 12-20-2011, 11:20 PM
Replies: 2
Views: 9,064
Posted By alexbmp
Thank you for your reply. So although I don't...

Thank you for your reply. So although I don't need the information right now, it can be important in some other pipeline I might take, right? :)
Forum: Bioinformatics 12-19-2011, 03:43 AM
Replies: 2
Views: 9,064
Posted By alexbmp
Question Setting @RG ID, PL, PU, LB, SM etc.

Hi all :)

When running bwa, I want the read group information to be implanted so that I can use the information in picard and GATK later.

I wrote down what I understood. Please point out if you...
Forum: Bioinformatics 11-11-2011, 08:57 PM
Replies: 12
Views: 6,082
Posted By alexbmp
Well, it works! Thank you all! :D

Well, it works! Thank you all! :D
Forum: Bioinformatics 11-10-2011, 04:27 AM
Replies: 4
Views: 6,441
Posted By alexbmp
@ Chipper Yes, I also agree using picard...

@ Chipper

Yes, I also agree using picard MergeSam instead of samtools merge.

However I found a case that picard MergeSam doesn't take many inputs (500 inputs) when options are default.

So in...
Forum: Bioinformatics 11-10-2011, 02:00 AM
Replies: 4
Views: 6,441
Posted By alexbmp
I used picard AddOrReplaceReadGroups.jar on this...

I used picard AddOrReplaceReadGroups.jar on this problem.

I think samtools also can add (actually, replace: by samtools reheader) read groups to your bam file.

For example:


Any other...
Forum: Bioinformatics 11-10-2011, 01:41 AM
Replies: 12
Views: 6,082
Posted By alexbmp
@ vang42: Actually, I haven't. That really is a...

@ vang42:
Actually, I haven't. That really is a good point! Thank you!

I'll try it on and update if it works :)
Forum: Bioinformatics 11-10-2011, 12:24 AM
Replies: 12
Views: 6,082
Posted By alexbmp
Not using splitted files really make the speed. ...

Not using splitted files really make the speed.

Still, it seems too slow to follow the pipeline GATK suggests...

I've changed my pipeline a little bit.

I reckoned that almost all the time...
Forum: Bioinformatics 11-04-2011, 10:41 PM
Replies: 12
Views: 6,082
Posted By alexbmp
Thank you all :) I'm trying it the other way. ...

Thank you all :) I'm trying it the other way.

The splicing seems to have taken most of the time.
Forum: Bioinformatics 11-04-2011, 06:19 PM
Replies: 12
Views: 6,082
Posted By alexbmp
@genericforms You mean 1) mappers like bwa,...

@genericforms

You mean 1) mappers like bwa, gsnap etc. can stream its output to samtools,

or 2) we could add another line after bwa aln, samse/pe to stream its output to samtools?

It really...
Forum: Bioinformatics 11-04-2011, 02:44 AM
Replies: 12
Views: 6,082
Posted By alexbmp
model name : AMD Opteron(tm) Processor 6172 ...

model name : AMD Opteron(tm) Processor 6172
cpu MHz : 2100.034

I think samtools sort takes so long probably because I divided my .bam alignment output into 500 pieces... (before...
Forum: Bioinformatics 11-03-2011, 11:30 PM
Replies: 12
Views: 6,082
Posted By alexbmp
GATK pipeline runtime

I wonder if I'm doing the things right; it takes so long.

I'm going to find SNPs for about 100 giga bps for the human genome.

After alignment, I processed my reads with samtools, picard and...
Forum: Bioinformatics 11-01-2011, 05:21 PM
Replies: 13
Views: 7,585
Posted By alexbmp
Wow! Really? :) It'll be so nice! My e.mail...

Wow! Really? :)

It'll be so nice! My e.mail is alex2bmp@gmail.com

It will help me a lot. Thank u so much!
Forum: Bioinformatics 11-01-2011, 03:27 PM
Replies: 13
Views: 7,585
Posted By alexbmp
Thank you for your reply. ;) The thing is, I...

Thank you for your reply. ;)

The thing is, I have to get an older version (dbSNP of hg18 like dbSNP130),
but I don't think it's on the web.
Forum: Bioinformatics 11-01-2011, 02:35 AM
Replies: 13
Views: 7,585
Posted By alexbmp
Does anybody know how to convert dbsnp to .vcf (variant calling format)?

The title implies my core question.

Does anybody know how to convert dbsnp to .vcf (variant calling format)?

I've downloaded dbsnp from UCSC annotation site,

but I wonder if there is any...
Forum: SOLiD 10-31-2011, 07:22 PM
Replies: 12
Views: 7,344
Posted By alexbmp
I was wondering this, too. Thanks for your...

I was wondering this, too. Thanks for your information!! :)
Forum: Bioinformatics 10-28-2011, 10:04 PM
Replies: 2
Views: 6,504
Posted By alexbmp
This is strange. You are right, when...

This is strange.

You are right, when soft-clipping occurs 5 more bases should be on the reads (in this case the terminal side).

The Funny thing is, that your read and score lengths don't match....
Forum: Bioinformatics 10-27-2011, 05:54 PM
Replies: 4
Views: 3,661
Posted By alexbmp
I got this quote from lh3: ...

I got this quote from lh3:
http://seqanswers.com/forums/showthread.php?t=3017

lh3 mentions that though XM:i:# can seem nonoptimal, it actually isn't;
lh3 says that such "seemingly nonoptimal"...
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