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Search: Posts Made By: Yilong Li
Forum: Bioinformatics 04-10-2012, 05:35 AM
Replies: 12
Views: 4,588
Posted By Yilong Li
@Heisman speaking from my own experience which...

@Heisman
speaking from my own experience which might be incorrect...: read depth algorithms designed for WGS data tend to be very noisy in exome data due to an additional source of noise coming from...
Forum: Bioinformatics 04-10-2012, 05:12 AM
Replies: 1
Views: 1,243
Posted By Yilong Li
Well you won't be able to know for sure whether a...

Well you won't be able to know for sure whether a variant is somatic or germ-line, since you don't know what the germline looked like...

Could you do something like: get a confident set of...
Forum: Bioinformatics 04-10-2012, 04:27 AM
Replies: 15
Views: 10,844
Posted By Yilong Li
I have used recalibration with human data, but...

I have used recalibration with human data, but haven't done any formal comparisons on its effects. I do know someone who did little bit of comparisons where it did seem that recalibration had little...
Forum: Bioinformatics 09-20-2011, 01:40 PM
Replies: 1
Views: 4,584
Posted By Yilong Li
Hey, we've seen a similar rise of adaptor...

Hey,

we've seen a similar rise of adaptor kmers towards the ends of the sequences. We haven't done anything formal analysis, but since we got paired-end sequences, we've been able to align the...
Forum: Bioinformatics 08-26-2011, 01:34 AM
Replies: 36
Views: 15,079
Posted By Yilong Li
We have done some alignments with Stampy and seen...

We have done some alignments with Stampy and seen the exact same problem of adjacent insertions and deletions. Also, sometimes Stampy seems to align the reads with weird indels, and they do not seem...
Forum: Bioinformatics 08-06-2011, 07:12 AM
Replies: 366
Views: 200,755
Posted By Yilong Li
Hi Simon, Have you published FastQC anywhere...

Hi Simon,

Have you published FastQC anywhere yet? Any idea how I should make a reference to it?
Forum: Bioinformatics 07-01-2011, 02:37 AM
Replies: 2
Views: 3,192
Posted By Yilong Li
Hi xysheep, I asked this from SOAPdenovo...

Hi xysheep,

I asked this from SOAPdenovo support back some time ago, and they told me that the map function only works with paired end reads. Hope this helps you!

Yilong
Forum: Bioinformatics 06-03-2011, 05:41 AM
Replies: 2
Views: 3,192
Posted By Yilong Li
Question SOAPdenovo map question

Dear fellow sequencers,

I am trying to assemble some reads using SOAPdenovo and map the reads to the assembled contigs. In SOAPdenovo, there is a utility SOAPdenovo map, that is supposed to do...
Forum: Bioinformatics 06-03-2011, 05:32 AM
Replies: 3
Views: 3,179
Posted By Yilong Li
Check...

Check ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/alignment.index. There should be all alignments available from 1000G repository atm and some annotation like the population of origin. And also the...
Forum: Bioinformatics 04-14-2011, 10:50 AM
Replies: 4
Views: 5,327
Posted By Yilong Li
Thanks for the amazing program, I've been looking...

Thanks for the amazing program, I've been looking for such a program for a very long time!

One question, will bedtools perform faster (esp. coverageBed or intersectBed), if the input BED or BAM...
Forum: Bioinformatics 04-13-2011, 01:10 AM
Replies: 6
Views: 4,013
Posted By Yilong Li
Yeah I think at least in my case the Q29 reads...

Yeah I think at least in my case the Q29 reads got overrepresented because in my set I only had reads that needed help from their mate to be mapped. Rather than read been too short, I think a more...
Forum: Bioinformatics 04-12-2011, 06:54 AM
Replies: 6
Views: 4,013
Posted By Yilong Li
I recently extracted from my BWA aligned BAM file...

I recently extracted from my BWA aligned BAM file all reads that were trimmed from 5'-end for at least 8 bp. This is (please correct me if I'm wrong) indicative of the fact that the read could be...
Forum: Bioinformatics 04-06-2011, 05:02 AM
Replies: 0
Views: 4,420
Posted By Yilong Li
Is there a but in BWA 3'-end trimming?

I got the following lines in the BAM file produced from BWA mapping using -q 6. It seems that the soft clipping in the CIGAR field is reporting one base less than should have been trimmed by the BWA...
Forum: Bioinformatics 04-05-2011, 01:07 PM
Replies: 7
Views: 3,498
Posted By Yilong Li
Yes, I fully agree that this particular position...

Yes, I fully agree that this particular position has so many dubious factors that it is unlikely to be a true variant :).

However, currently we would like to find recurrent variants present in...
Forum: Bioinformatics 04-05-2011, 12:24 PM
Replies: 7
Views: 3,498
Posted By Yilong Li
I have done realignment but not base quality...

I have done realignment but not base quality recalibration.

If I understood correctly though, GATK UG calls variants from a bam file and does not know whether the realignment or recal has been...
Forum: Bioinformatics 04-05-2011, 09:58 AM
Replies: 7
Views: 3,498
Posted By Yilong Li
Sorry, I didn't provide enough information...

Sorry, I didn't provide enough information regarding the situation. I ran GATK UG using --min_base_quality 1 (so all the grey C bases should have been included in the calling). Data is from Illumina....
Forum: Bioinformatics 04-05-2011, 07:18 AM
Replies: 7
Views: 3,498
Posted By Yilong Li
"Obvious variant" missed by GATK UnifiedGenotyper

Hi all,

We have noticed in our lab that GATK UnifiedGenotyper misses some variants (as one shown in the IGV figure below) that seem reasonably obvious with good alt. allele counts.

I ran GATK...
Forum: Bioinformatics 04-05-2011, 07:01 AM
Replies: 0
Views: 1,838
Posted By Yilong Li
VCF index creation doesn't finish

I have encountered the following problem several times. When running GATK RealignerTargetCreator, the program attempts to create the indices for the input VCFs.

With some of my VCFs, the index...
Forum: Bioinformatics 03-20-2011, 10:30 AM
Replies: 7
Views: 6,164
Posted By Yilong Li
Try running picard FixMateInformation (or...

Try running picard FixMateInformation (or something like that) after ViewSam to correct the mate pair information in the resulting sam files.

I guess it is not unexpected to see fragments where...
Forum: Bioinformatics 03-20-2011, 10:27 AM
Replies: 2
Views: 2,541
Posted By Yilong Li
I've had similar problems under Linux, but with...

I've had similar problems under Linux, but with different programs. During scaffolding in Velvet, the program stops progressing even though top shows that it is still fully running. Oddly enough,...
Forum: Bioinformatics 03-02-2011, 11:56 PM
Replies: 8
Views: 5,137
Posted By Yilong Li
The N's you're seeing are probably the masked...

The N's you're seeing are probably the masked telomere of chromosome 1. Trying pressing 'g' in tview and going to a random location like 1:10000000 to see if you can see any ref sequence there.
...
Forum: Bioinformatics 02-28-2011, 06:33 AM
Replies: 36
Views: 15,079
Posted By Yilong Li
I am trying to run -glm DINDEL with -A...

I am trying to run -glm DINDEL with
-A DepthOfCoverage
-A AlleleBalance
and try to get the allele balance info to the output, but they don't seem to be there.

So I am interested in finding...
Forum: Bioinformatics 02-28-2011, 05:12 AM
Replies: 5
Views: 2,791
Posted By Yilong Li
Bump. Please share any ideas!

Bump. Please share any ideas!
Forum: Bioinformatics 02-26-2011, 12:45 PM
Replies: 3
Views: 2,588
Posted By Yilong Li
In mpileup in the INFO field, there's the AF1...

In mpileup in the INFO field, there's the AF1 subfield that'll tell you the frequency.

In GATK UnifiedGenotyper the same info can be found in the last field in the AD subfield.

At least this...
Forum: Bioinformatics 02-26-2011, 12:10 PM
Replies: 3
Views: 2,588
Posted By Yilong Li
Have a look at samtools mpileup and GATK...

Have a look at samtools mpileup and GATK UnifiedGenotyper, I think they can do what you want.
Showing results 1 to 25 of 41

 


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