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Search: Posts Made By: frankyue50
Forum: Bioinformatics 02-19-2014, 10:10 AM
Replies: 4
Views: 1,176
Posted By frankyue50
I guess that's the reason... I print out the bed...

I guess that's the reason... I print out the bed file from bam and things worked out.

Thanks, GenoMax!
Forum: Bioinformatics 02-19-2014, 09:55 AM
Replies: 4
Views: 1,176
Posted By frankyue50
this is from samtools view reads.bam: name...

this is from samtools view reads.bam:
name 163 1 10001 29 39S25M37S = 10026 126 ...
Looks like a normal bam file to me
Forum: Bioinformatics 02-19-2014, 09:32 AM
Replies: 4
Views: 1,176
Posted By frankyue50
exon coverage by coverageBed

Hello everyone,

So I just want to compute the average coverage per base for our exome-seq. First I collected all the exons in a bed file, say exon.bed and it looks like this:

chr1 11873 12227...
Forum: General 12-09-2013, 11:49 AM
Replies: 6
Views: 3,005
Posted By frankyue50
I am thinking the same thing. I run my fastqc on...

I am thinking the same thing. I run my fastqc on a linux server ... maybe I should fire up GUI and directly run it on my iMAC
Forum: General 12-09-2013, 10:51 AM
Replies: 6
Views: 3,005
Posted By frankyue50
Thanks for the response. I did get a *fastq.zip...

Thanks for the response. I did get a *fastq.zip file, but when I failed to unzip it, it gave me this error msg:
End-of-central-directory signature not found. Either this file is not
a zipfile,...
Forum: General 12-09-2013, 05:58 AM
Replies: 6
Views: 3,005
Posted By frankyue50
Since this is a pair-ended seq, I run the fastqc...

Since this is a pair-ended seq, I run the fastqc on both fastqs at the same time, still errors ...
Forum: General 12-08-2013, 01:04 PM
Replies: 0
Views: 2,178
Posted By frankyue50
gatk -nt option

My understanding is tha -nt at machine level from GATK primer and -nct is at core level.

It seems that -nt 4 -nct 4 and -nt 1 -nct 16 both require 16 cores, but -nt 4 -nct 4 indeed asked for four...
Forum: General 12-08-2013, 12:26 PM
Replies: 6
Views: 3,005
Posted By frankyue50
weird fastqc error

Here is how I run it: fastqc file.fastq -o output

Results:
....
Approx 95% complete for 1.fastq
Approx 100% complete for 1.fastq
Analysis complete for 1.fastq
Failed to process file 1.fastq...
Forum: Bioinformatics 11-25-2013, 12:54 PM
Replies: 2
Views: 6,689
Posted By frankyue50
Anyway, here is what I did: java -Xmx4g -jar...

Anyway, here is what I did:

java -Xmx4g -jar GenomeAnalysisTK.jar -l INFO -R hg19.fa -knownSites 00-All.vcf -I input.nodup.realigned.fixed.bam -T BaseRecalibrator -cov ReadGroupCovariate -cov...
Forum: Bioinformatics 11-25-2013, 11:50 AM
Replies: 2
Views: 6,689
Posted By frankyue50
GATK recalibration confused, one step or two step?

Just based my reading
Previously, it was:
Quote:
java -Xmx4g -jar GenomeAnalysisTK.jar -l INFO -R hg19.fa --DBSNP dbsnp132.txt -I input.marked.realigned.fixed.bam -T CountCovariates -cov...
Forum: Bioinformatics 11-22-2013, 06:18 AM
Replies: 3
Views: 4,864
Posted By frankyue50
Geez! You are so good! Owe you a big one!

Geez! You are so good! Owe you a big one!
Forum: Bioinformatics 11-21-2013, 07:02 PM
Replies: 3
Views: 4,864
Posted By frankyue50
can anyone help? or point a direction?

can anyone help? or point a direction?
Forum: Bioinformatics 11-21-2013, 04:15 PM
Replies: 3
Views: 4,864
Posted By frankyue50
bwa sampe: the read group line is not started with @RG

Has anyone seen this error before? Just some standard pair-endedexome-seq

First I did:
bwa aln -t 12 hg19.fa R2.fastq > R2.fastq.sai
bwa aln -t 12 hg19.fa R1.fastq > R1.fastq.sai

tried to...
Forum: Bioinformatics 06-06-2011, 11:09 AM
Replies: 2
Views: 2,726
Posted By frankyue50
you need to add it to your PATH, for example...

you need to add it to your PATH, for example .bash_profile
Forum: Bioinformatics 03-14-2011, 03:35 PM
Replies: 3
Views: 2,181
Posted By frankyue50
at least for the current version, I remember a...

at least for the current version, I remember a read can be mapped to as many as 20 locations.
Forum: Bioinformatics 03-14-2011, 03:32 PM
Replies: 12
Views: 6,481
Posted By frankyue50
got the same error msg. wonder if it matters...

got the same error msg. wonder if it matters ............
Forum: Bioinformatics 03-03-2011, 10:19 AM
Replies: 13
Views: 4,157
Posted By frankyue50
But you provided a gtf file ... We were talking...

But you provided a gtf file ... We were talking about the transcriptome assembly.
Forum: Bioinformatics 03-02-2011, 03:28 PM
Replies: 13
Views: 4,157
Posted By frankyue50
In some cases, I have seen cufflinks give more 1...

In some cases, I have seen cufflinks give more 1 million transcript. But I checked the authors original paper, they only predicted less 30000 transcript ...
Forum: Bioinformatics 03-02-2011, 02:15 PM
Replies: 3
Views: 2,230
Posted By frankyue50
I don't think any programs should give you...

I don't think any programs should give you different result on the same set of data, unless you need to generate some random number ...
Forum: Bioinformatics 02-28-2011, 10:42 PM
Replies: 1
Views: 1,168
Posted By frankyue50
Ok, just an update. I re-run the analysis with...

Ok, just an update. I re-run the analysis with pair-end sequencing. The result is similar. It gave 600,000 transcript. I just don't think it's possible... Does anyone have any suggestions?
Forum: Bioinformatics 02-28-2011, 08:32 AM
Replies: 1
Views: 1,168
Posted By frankyue50
number of transcript by cufflinks

Hi, guys, I am using cufflinks to assemble mouse transcriptome, and it gives me 500,000 transcript. My RNA-seq is single end 36 bases. can this result be trusted?

Usually how many transcript can...
Forum: Bioinformatics 10-11-2010, 03:37 PM
Replies: 1
Views: 1,358
Posted By frankyue50
should RNA-seq use monoclonal reads

hi, guys, I was wondering what's your take on this. Tophat will accept reads that are mapped up to 20 locations and take a fraction for each location. Well, this could be helpful to identify...
Forum: Bioinformatics 10-04-2010, 08:33 AM
Replies: 4
Views: 1,516
Posted By frankyue50
thanks, kmcarr! glad to see I am not the only one...

thanks, kmcarr! glad to see I am not the only one see this.
Forum: Bioinformatics 10-03-2010, 12:42 AM
Replies: 4
Views: 1,516
Posted By frankyue50
I just tested it again. I cannot imagine how can...

I just tested it again. I cannot imagine how can I mess up the installation. All I did is: download the source file, unzip it and:

./configure --prefix=/home/myusername
make
make install
...
Forum: Bioinformatics 10-02-2010, 03:10 PM
Replies: 4
Views: 1,516
Posted By frankyue50
something wrong with tophat-1.0.14 version, don't use it

Hi, guys, I was trying the "new" version of tophat and found that it has 3708 lines.

But in the old version, 1.0.13 it only has around 1600 lines. so I wonder WTH is going on? I open the tophat...
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