User: b10hazard

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b10hazard0
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Posts by b10hazard

<prev • 7 results • page 1 of 1 • next >
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how do you do variant calling on tumor samples without a normal tissue sample
... I read a paper on somatic variant callers for tumor tissue and I have a few questions. The variant callers seem to work by subtracting the variants found in normal tissue from tumor tissue. Here is the article. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4803342/ My questions are... Is there a ...
next-gen snp written 8 months ago by b10hazard0 • updated 6 months ago by Biostar ♦♦ 20
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Comment: C: Are there any aligners that enable me to align sense strands only to a sense str
... Just what I needed. Thanks! ...
written 8 months ago by b10hazard0
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Are there any aligners that enable me to align sense strands only to a sense strand reference sequence
... Is there an aligner that allows me to ignore reverse complement alignments. For example, my reference sequence I'm aligning to will always be single stranded sense DNA (the antisense strand is selectivily degraded). Also, the fragments I'm aligning are always going to be single stranded sense DNA ...
next-gen alignment bwa sequencing written 8 months ago by b10hazard0 • updated 8 months ago by valdirbarth20
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Comment: C: How do I retrieve a specific region of a chromosome from a local blast database
... Ah, you're correct, that was it. The fasta has chr1 as the record ID. It works now. Thanks! ...
written 12 months ago by b10hazard0
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Comment: C: How do I retrieve a specific region of a chromosome from a local blast database
... I install samtools using apt-get (I am on ubuntu). I ran the command you posted but it did not produce a fasta file. All I got was this output on the command line.... >1:24957500-24958000 I grabbed the whole assembly because I need to use it for other projects that involve blast searches. ...
written 12 months ago by b10hazard0
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How do I retrieve a specific region of a chromosome from a local blast database
... I created a local blast database of the human genome (version GRCh38) using a fasta file I downloaded from NCBI. The fasta file records are named after the chromosomes so chromosome 1 has the record "chr1 1". I would like to query this database to get base pairs 24957500-24958000 in a fasta file f ...
blast written 12 months ago by b10hazard0
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How do I download entire human genome for local blast formatting and searching?
... I'm trying to make a copy of the entire human genome for local blast queries on my machine. I understand that I need to download it from the NCBI FTP server here... ftp://ftp.ncbi.nih.gov/genomes/Homo_sapiens After downloading it I need to format it into a database that blast can search. I do t ...
ncbi blast written 15 months ago by b10hazard0

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