User: Jackie

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Jackie30
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30
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New User
Location:
United States
Last seen:
5 days, 17 hours ago
Joined:
4 years, 8 months ago
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Posts by Jackie

<prev • 20 results • page 1 of 2 • next >
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Difference between the two models in manta
... What is the difference between the manta disease model (--tumorBam) and germline model (--bam)? i.e, different calling algorithms, different filtering criteria? Is there some detailed documentation on that? Thanks ...
manta rna-seq written 6 days ago by Jackie30
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Questions about the splitting/spannings reads reported by manta
... Has anyone used the SV caller manta? I have a couple of questions regarding the splitting/spanning reads reported by manta: 1) In the manta output 'diploidSV.vcf', there are PR and SR tags, which mean 'Spanning paired-read support for the ref and alt alleles in the order listed' and 'Split reads fo ...
manta splitting reads spanning reads rna-seq written 6 days ago by Jackie30
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How to align reads using bowtie against multiple customized reference files
... Hi, I am trying to use Bowtie to align RNA-seq fastq files to a set of small reference fasta files (i.e., ribosomal reference, mitochondrial reference, all for human). I've learned some groups have done that, but technically, I don't know how to implement that. As far as I know, Bowtie does not d ...
bowtie written 9 days ago by Jackie30
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Comment: C: Alignment stats summary by STAR aligner, please help!
... Thanks apa@stowers for the very detailed response, that helps. Yes, I found the spliced alignment particularly confusing. And, I also tried samtools flagstat for stats on read1/read2 separately, seems it would not give you the number same as in STAR log output. I.e., the total number of reads in ea ...
written 10 days ago by Jackie30
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Alignment stats summary by STAR aligner, please help!
... Hi, I am using STAR to align RNA-seq data, and I would like to make a QC metrics report out of the STAR logs. I want to do something like below: Total Aligned Reads for read1 and read 2 (% Reads) Abundant Reads for read1 and read 2 (% Reads) Unaligned Reads for read1 and read 2 (% Reads) Reads ...
alignment qc star rna-seq written 11 days ago by Jackie30
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Answer: A: Tophat-fusion-post running errors
... Hi, Can anyone share some experience or provide some insights to this issue? Thanks! ...
written 7 weeks ago by Jackie30
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Tophat-fusion-post running errors
... Hi, I am running tophat-fusion-post using this command line: ./tophat-fusion-post -p 8 --num-fusion-reads 1 --num-fusion-pairs 2 --num-fusion-both 5 / The tophat-fusion output folder is in the same directory where I am running the command line. and I got below error messages: Traceback (most re ...
tophat-fusion-post bowtie python error written 7 weeks ago by Jackie30
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Answer: A: Oncofuse: Prediction Of Driver Gene Fusions From Ngs Data
... Hi Mikhail, I have 2 questions about ONCOFUSE: 1) Is the annotation file in ONCOFUSE from UCSC refseq? I use NCBI reference/annotation files for the reads alignment and breakpoint annotation, and it seems there are a few inconsistencies between the ONCOFUSE annotation and NCBI annotation. i.e., thi ...
written 9 weeks ago by Jackie30
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Pindel vcf tag HOMLEN?
... Hi, I have a question about the VCF tag 'HOMLEN' that Pindel generates. In the header description, it says HOMLEN is the 'Length of base pair identical micro-homology at event breakpoints'. I wonder if it's the same as the 'homopolymer run length'? If not exactly the same, then is there a relation ...
vcf homlen hrun homopolymer run pindel written 5 months ago by Jackie30 • updated 3 months ago by Biostar ♦♦ 10
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Comment: A: Tophat chromosome position greater than chromosome size
... Can anyone help with this? ...
written 5 months ago by Jackie30

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