User: dyollluap

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dyollluap300
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USA, California, Bay Area
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Posts by dyollluap

<prev • 42 results • page 1 of 5 • next >
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Comment: C: Number of SNPs in VCF
... Based on previous q&a on the comments, there's an assumption of non-perfect compliance to vcf specification. My guess/interpretation without seeing any example lines, the breed is labeled in each row and the OP wants a count / sub-total of variants for each breed. ...
written 22 months ago by dyollluap300
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Answer: A: Number of SNPs in VCF
... I think the easiest option is to grep each breed and output the count: grep 'SIM001' mymultisample.vcf | wc If you have a list of breeds in your multisample vcf, create a for loop: for breed in $( ...
written 22 months ago by dyollluap300
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Answer: A: alignment used for CCLE RNA-seq
... It's in the associated analysis metadata files: tophat N/A tophat v1.4.1 tophat.sh -o tophat_out --num-threads $NSLOTS --mate-inner-dist 300 --mate-std-dev 500 --no-sort-bam --no-convert-bam --GTF Homo_sapiens_assembly19.gtf --transcriptome-index annotation Homo_ ...
written 22 months ago by dyollluap300
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Comment: C: VEP and Annovar Annotation
... Try with --per_gene and --coding_only to avoid the thousands of transcripts problem. ...
written 2.2 years ago by dyollluap300
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Comment: C: VEP and Annovar Annotation
... which VEP options are you running? ...
written 2.2 years ago by dyollluap300
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Comment: C: Miseq Genomic DNA analysis
... which species are you sequencing? ...
written 2.2 years ago by dyollluap300
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Answer: A: esiRNA sequences in Drosophila
... Try [modENCODE][1] Total RNA-seq datasets for Drosophila - much of the higher level analysis results has been long included in FlyBase, however it's based on Total RNA time course series, so it's likely to have many ncRNA if you're looking for it specifically within the bams. Also check if anything ...
written 2.2 years ago by dyollluap300
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Answer: A: IGV error: Error loading SAM header: For sequence 34711, text and binary have di
... Usually I see that different lengths in file error when different versions of the reference assembly have been used in whatever process is being performed. In this case, if the reference.fa you used for building a bam index is different from the original sam alignment, you get this error. ...
written 2.3 years ago by dyollluap300
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Answer: A: Is the database, 'Yeast Nucleosome Atlas (YNA)', reliable?
... The friendly folks at the [SGD][1] will probably have a strong (and very conservative) opinion about YNA... they do a manual curation process and are very familiar with some of the intricate details of the underlying studies. The SGD helpdesk is fairly active and they usually provide careful and com ...
written 2.3 years ago by dyollluap300
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Answer: A: which annotation to use and is it advisable to use bam to fastq
... 1. If you have the resources I'd suggest doing both mm9 and mm10. Future proofing and also back compatible using the same pipeline. 2. You should find the relevant sequence run details, instrument data, etc., in the bam header @RG lines which can be used to deconvolute the bams to original fastq. ...
written 2.3 years ago by dyollluap300

Latest awards to dyollluap

Popular Question 10 months ago, created a question with more than 1,000 views. For any recommended tools for batch effect and normalization not written in R?
Scholar 22 months ago, created an answer that has been accepted. For A: How to get rs number for the variants list?
Scholar 2.3 years ago, created an answer that has been accepted. For A: How to get rs number for the variants list?
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: where can I find the "code table report" for TCGA barcode?
Scholar 2.3 years ago, created an answer that has been accepted. For A: How to get rs number for the variants list?
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: where can I find the "code table report" for TCGA barcode?
Scholar 2.6 years ago, created an answer that has been accepted. For A: How to get rs number for the variants list?
Scholar 2.7 years ago, created an answer that has been accepted. For A: How to get rs number for the variants list?
Supporter 2.8 years ago, voted at least 25 times.

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