User: emblake

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emblake40
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New User
Location:
United States
Last seen:
6 months, 2 weeks ago
Joined:
1 year, 2 months ago
Email:
e****@nova.edu

Posts by emblake

<prev • 29 results • page 1 of 3 • next >
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Comment: C: HLA typing WGS data
... I misunderstood - my mistake. That makes sense. Thank you. ...
written 9 months ago by emblake40
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Comment: C: HLA typing WGS data
... Thanks for your input. The estimated HLA type from the software shows my sample is heterozygous E*01:03:01:01/E*01:01:01:01. I subset the reads matching E*01:03:01:01 by `samtools view -h input.bam HLA:HLA00936 > HLA00936.bam` and then used MUSCLE to align those sequences against the nuclear cod ...
written 9 months ago by emblake40
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HLA typing WGS data
... I have HLA typed whole genome sequencing data using [HLA-VBSeq][1]. Reads were first aligned to hg19 with BWA-MEM, then reads aligning to all HLA loci and unmapped reads were extracted from the bam file using samtools. The extracted reads were then combined and re-aligned to the collection of all th ...
wgs hla samtools bwa written 9 months ago by emblake40 • updated 9 months ago by dario.garvan370
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Comment: C: ENSEMBL masked GTF file?
... Got it. Is there a better or recommended alternative to masking/removing RNA entries than generating a new GTF file? ...
written 10 months ago by emblake40
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Comment: C: ENSEMBL masked GTF file?
... Thanks! How would I do the latter? ...
written 10 months ago by emblake40
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Comment: C: ENSEMBL masked GTF file?
... Yes, I'm just not sure how to ignore those counts. Would something like `grep -wv rRNA,tRNA Homo_sapiens.GRCh38.87.gtf | Homo_sapiens.GRCh38.87.masked.gtf` work to generate a masked GTF file for input into featureCounts? ...
written 10 months ago by emblake40
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ENSEMBL masked GTF file?
... Is there an ENSEMBL tRNA, rRNA masked GTF file available for GRCh38.p7? If not, would someone kindly provide info on creating one? I'm using STAR to align PE RNA-seq data and featureCounts for read counting. Thank you! ...
ensembl rna-seq written 10 months ago by emblake40
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Comment: C: Empty ENSEMBL gene annotations
... Thanks. I figured as much, but I've seen research removing data that doesn't contain official gene symbols: https://f1000research.com/articles/5-1438/v1. Just curious what the consensus is on this type of filtering. ...
written 12 months ago by emblake40
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Empty ENSEMBL gene annotations
... I'm using org.Hs.eg.db to annotatate ENSEMBL gene IDs from a read counts matrix, and after my list is created, I have ~3700 that have 'NA' for the annotation. If I keep these unannotated genes, perform DE testing in edgeR, and retrieve my topTags, I see quite a few of the unannotated genes in this ...
R annotations rna-seq ensembl written 12 months ago by emblake40
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Comment: C: Download gene list associated with GO terms from DAVID
... I would like to download GeneSCF to give it a try, but your [website][1] isn't working. Is it me or is there an issue? Thanks. [1]: http://genescf.kandurilab.org/ ...
written 12 months ago by emblake40

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