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Search: Posts Made By: KaiYe
Forum: Bioinformatics 05-26-2015, 06:48 AM
Replies: 147
Views: 57,820
Posted By KaiYe
Pindel marks a read as duplicated if both read...

Pindel marks a read as duplicated if both read pairs are identical. For the first event, both read sequences and the their mates' mapping positions are the same. Thus they are all marked as...
Forum: Bioinformatics 02-18-2015, 07:38 AM
Replies: 18
Views: 5,915
Posted By KaiYe
Pindel is able to call indels from many samples...

Pindel is able to call indels from many samples at the same time and give you indication of which samples are the carriers. The new pindel2vcf gives you a clean way to view the result with the...
Forum: Bioinformatics 02-12-2015, 06:40 AM
Replies: 3
Views: 1,753
Posted By KaiYe
Is it possible to send me the log file or console...

Is it possible to send me the log file or console output to my email kye@genome.wustl.edu?
Forum: Bioinformatics 02-12-2015, 06:28 AM
Replies: 3
Views: 1,753
Posted By KaiYe
can you tell me your Pindel version? You could...

can you tell me your Pindel version? You could split calculation by 5MB per job. Sometimes there is extreme high coverage at a few small regions. This causes maximum memory usage going high.

Kai
Forum: Bioinformatics 02-07-2015, 06:45 PM
Replies: 4
Views: 3,634
Posted By KaiYe
use samtools 0.1.18

use samtools 0.1.18
Forum: Bioinformatics 12-01-2014, 12:26 PM
Replies: 1
Views: 1,704
Posted By KaiYe
If you extract reads and then push them through...

If you extract reads and then push them through Pindel, you will not get read count for ref supporting reads. you could use -i to see whether things work out.
Forum: Bioinformatics 09-24-2014, 07:43 AM
Replies: 147
Views: 57,820
Posted By KaiYe
interchromosomal events will not be affected if...

interchromosomal events will not be affected if split per chr.
Forum: Bioinformatics 09-24-2014, 06:33 AM
Replies: 147
Views: 57,820
Posted By KaiYe
For exome data, you could use -x 2 or even -x 1...

For exome data, you could use -x 2 or even -x 1 to speed up. Which version are you using? Recently I changed the code and remove one memory leak.

You'd better run jobs per chr and maximum 4...
Forum: Bioinformatics 08-12-2014, 07:12 AM
Replies: 7
Views: 2,397
Posted By KaiYe
It is heuristic to choose 2 times insert size....

It is heuristic to choose 2 times insert size. Both maximum and minimum substring define the range of read being split while mapping back to the reference genome correctly. Due to local repeats...
Forum: Bioinformatics 08-08-2014, 07:17 AM
Replies: 7
Views: 2,397
Posted By KaiYe
please check my ppt at...

please check my ppt at http://www.ebi.ac.uk/~kye/pindel/pindel_ismb2009_june28.ppt

There is one animation in the slides about the mapping procedure. let me know if you have any questions after...
Forum: Bioinformatics 08-07-2014, 05:26 AM
Replies: 7
Views: 2,397
Posted By KaiYe
DNA fragments are double stranded and the read...

DNA fragments are double stranded and the read data generated will map to one of the strand. And DNA is synthesized from 5' to 3'. Please google DNA strand and I put one search result below, although...
Forum: Bioinformatics 08-05-2014, 06:08 AM
Replies: 1
Views: 1,210
Posted By KaiYe
Pindel's memory usage is linear to the data it...

Pindel's memory usage is linear to the data it needs to realign. If you have more samples or coverage is high, you will observe higher memory footprint. As the numbers of variants and repetitive...
Forum: Bioinformatics 07-24-2014, 02:11 PM
Replies: 3
Views: 2,403
Posted By KaiYe
Pindel is multi-threaded when processing reads...

Pindel is multi-threaded when processing reads but single thread while loading reference genome and read bam files.
Forum: Bioinformatics 07-07-2014, 05:47 AM
Replies: 11
Views: 8,659
Posted By KaiYe
If you convert output file to vcf, the ref and...

If you convert output file to vcf, the ref and alt alleles will be reported. Indeed the deleted sequence is not displayed in the raw output but this was the way I designed.
Forum: Bioinformatics 06-13-2014, 07:59 AM
Replies: 3
Views: 1,684
Posted By KaiYe
can you get the latest version to test again...

can you get the latest version to test again using demo data? There was one read selection step changed recently and it does slow down Pindel dramatically. Now I have modified it. You should be able...
Forum: Bioinformatics 06-13-2014, 07:56 AM
Replies: 15
Views: 5,143
Posted By KaiYe
as we communicated by email, you can distribute...

as we communicated by email, you can distribute your calculation with -c chr:start-end. You might use 4 threads per job and maximize the number of jobs running at the same time. Pindel will only get...
Forum: Bioinformatics 06-08-2014, 04:42 AM
Replies: 3
Views: 1,684
Posted By KaiYe
can you show me how you run Pindel on the demo...

can you show me how you run Pindel on the demo data or what you mean "I run the demo run code"? Pindel is realigning reads than processing the alignment result from mapper so that it is expected to...
Forum: Bioinformatics 06-02-2014, 08:47 AM
Replies: 15
Views: 5,143
Posted By KaiYe
some bugs removed and a few performance...

some bugs removed and a few performance optimization.
Forum: Bioinformatics 06-02-2014, 08:46 AM
Replies: 15
Views: 5,143
Posted By KaiYe
you could use dropbox or box

you could use dropbox or box
Forum: Bioinformatics 05-30-2014, 10:10 AM
Replies: 15
Views: 5,143
Posted By KaiYe
hi GFP, The running log file looks fine to...

hi GFP,

The running log file looks fine to me. I noticed the string "unaligned" in your file name. Is your bam file complete without removing any reads?

send me some data to reproduce the...
Forum: Bioinformatics 05-29-2014, 06:47 AM
Replies: 15
Views: 5,143
Posted By KaiYe
so Pindel terminates when searches for...

so Pindel terminates when searches for inversions? How much memory it uses when existing? Can you run Pindel with -c to find the genomic region where it went wrong and extract the local data around....
Forum: Bioinformatics 05-28-2014, 07:21 PM
Replies: 15
Views: 5,143
Posted By KaiYe
can you tell me more about your data? Illumina,...

can you tell me more about your data? Illumina, paired-end? insert size?
Forum: Bioinformatics 05-24-2014, 05:00 AM
Replies: 15
Views: 5,143
Posted By KaiYe
your Pindel version? The latest version is 0.2.5...

your Pindel version? The latest version is 0.2.5 at github
Forum: Bioinformatics 04-29-2014, 07:25 AM
Replies: 11
Views: 8,659
Posted By KaiYe
upper and lower case define junction

upper and lower case define junction
Forum: Bioinformatics 04-29-2014, 07:23 AM
Replies: 1
Views: 2,440
Posted By KaiYe
You could do an awk selection based on the number...

You could do an awk selection based on the number of samples and the numbers of reads supporting the ALT. then filtering dbSNP entries and restrict homopolymer and micro satellite calls to regions...
Showing results 1 to 25 of 133

 


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