User: Wai Yi Leung

gravatar for Wai Yi Leung
Wai Yi Leung30
Reputation:
30
Status:
New User
Location:
Netherlands
Website:
http://geno.mics.io/
Twitter:
tweakboy
Last seen:
1 year, 8 months ago
Joined:
4 years ago
Email:
t*******@gmail.com

I'm a scientific software developer/engineer working on structural variation projects.

Posts by Wai Yi Leung

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Illumina X ten samples have phred scores out of range [0,41]
... Thank you for your elaborate answer. For our specific use-case, we are implementing a FastQ validator in our analysis pipeline to check the validity (and propagation to either continue / halt pipeline ). As we take the assumption the range is 0..41, our setup with the validation is not working for ...
written 21 months ago by Wai Yi Leung30
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Comment: C: Illumina X ten samples have phred scores out of range [0,41]
... Thank you for your reply. Technically, phred scored can consume the whole ASCII spectrum (to q=126 (127 is not printable?)) I would like to know to which spec the new scale is conforming. I cannot really read from the documentation that they defined a spec like Illumina 2.0 or so for this case I fo ...
written 21 months ago by Wai Yi Leung30
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Illumina X ten samples have phred scores out of range [0,41]
... In our lab we are working with Illumina X ten samples for quitte some time. Recently we were having a more indepth inspection on the sequences delivered from the Illumina X ten runs. We were looking into the phred scores from several samples and found phred scores which exceed the set bounderies ...
sequencing quality next-gen phred-encoding written 21 months ago by Wai Yi Leung30 • updated 21 months ago by Dan D6.2k
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Comment: C: Pindel :: terminate called after throwing an instance of 'std::out_of_range'
... The bam has an index. The issue is solved by using a correct Fasta file. (alignment used an other fasta file) Maybe this could be added to pindel, to warn a user whenever the supplied reference_fasta is not the same as stated in the header of a bamfile? ...
written 22 months ago by Wai Yi Leung30
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Pindel :: terminate called after throwing an instance of 'std::out_of_range'
... I've some difficulties running Pindel on a WGS bam (human genome GRCh38). I've no problems running pindel on bacteria samples i have (with same settings). The program crashes with the following message: ====== BAM file index  0 Bam file name   /data/700232000002.dedup.realign.bam Number of split- ...
software error pindel written 22 months ago by Wai Yi Leung30
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Comment: C: How to run pindel with multithreading?
... the -T option is correct Only when pindel is loading the genome it will use at most 1 thread. ...
written 3.3 years ago by Wai Yi Leung30
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Pindel segmentation fault in GetRealStart4Deletion
... Dear Kai, I found a possible bug in one of the functions: GetRealStart4Deletion. See a fragment from gdb: There are 0 split-reads mapped by aligner. report closeMappedReads search far ends Far end searching completed for this window. update FarFragName update FarFragName done save interchromsome ...
pindel written 3.3 years ago by Wai Yi Leung30 • updated 3.3 years ago by liangkaiye250

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