User: brismiller

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brismiller40
Reputation:
40
Status:
New User
Location:
Bellingham, WA, USA
Last seen:
3 months, 1 week ago
Joined:
3 years, 4 months ago
Email:
b*********@gmail.com

Posts by brismiller

<prev • 38 results • page 1 of 4 • next >
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Understanding BEDtools summary output
... Hey all, I am using Bedtools summary program to do some quick quality control steps on some bed files that I have generated. I have looked for the man page for this program but I cannot find it. I am trying to understand what each of the columns in the output means. Is there a man page somewhere ob ...
bedtools bed summary man written 3 months ago by brismiller40
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Comment: C: chromosome length .size file
... Thanks for that Pierre, I just found out that I could cut samtools fai f1 and f2 to get what I want. ...
written 4 months ago by brismiller40
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chromosome length .size file
... Hey all, I am trying to make a .size file that lists the length of each chromosome from a genome file (e.g. fasta file) Here is an example of the desired output: chr1 248956422 chr10 133797422 chr11 135086622 chr12 133275309 chr13 114364328 chr14 107043718 chr15 1019911 ...
genome size chromosome written 4 months ago by brismiller40 • updated 4 months ago by Pierre Lindenbaum131k
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Comment: C: GATK liftOver chain file for human_g1k_v37.fasta
... In the end I was unable to find a better chain file(s) for this conversion. But, if you stop and think about it, if your variants you are interested in are in protein coding regions (like mine are) then this should not affect your results as the g1k_v37 -> b37 -> hg19 conversion mainly affects ...
written 4 months ago by brismiller40
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ANNOVAR issue annotating vcf
... Hey all, I am trying to annotate some wgs variant data with minor allele frequencies from the GNOMAD database. I am tring to use ANNOVAR to do this, but I am running into some errors. executed: annotate_variation.pl -regionanno -dbtype gnomad_genome -outfile test_out -buildver hg38 n4k_EGAF21. ...
annover variant gnomad written 4 months ago by brismiller40
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Comment: C: unplaced, unlocalized, ... scaffolds from hg19 to GRCh38
... Was this resolved somewhere else besides this post? I am having the same issue but for lifting over variants ("LiftoverVcf Encountered a contig, 2_KI270773v1_alt that is not part of the target reference."). I am using the latest version of Picard, and the proper liftover file. Is the best way forwar ...
written 4 months ago by brismiller40
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Comment: C: GATK liftOver chain file for human_g1k_v37.fasta
... i just made a gatk post https://gatk.broadinstitute.org/hc/en-us/community/posts/360067939931-b37-to-hg38-liftover-issues I will keep this post updated as things progress ...
written 4 months ago by brismiller40
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GATK liftOver chain file for human_g1k_v37.fasta
... Hey all, is there a chain file that I can use to lift over variants from human_g1k_v37.fasta to hg38? I ran GATK's LiftoverVcf using the hg19ToHg38.over.chain file and it worked for most of the variants in the test files that I ran it on. ~99.93%, but I was just wondering if anyone knew of a speci ...
genome gatk alignment sequencing written 4 months ago by brismiller40 • updated 3 months ago by Biostar ♦♦ 20
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Comment: C: replace fasta headers with another name in a text file
... Here is a modified version that takes in a tab-delimited lookup table of headers to replace, this works even if only a subset of the headers need replacing and it also works if the headers that need replacing are in a different order than the entries in the lookup table. [edit] I just tested this a ...
written 5 months ago by brismiller40
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LiftoverVcf no output
... Hey all, I am trying to run Picard's LiftoverVcf to lift over a hg19 to hg38, but there is no output. It runs with no errors, but it doesn't make the output files. Any help would be appreciated. Here is the relevant section of the script used. I even tried unzipping all input files, but no output ...
genome assembly picard liftover sequencing written 5 months ago by brismiller40

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Popular Question 5 months ago, created a question with more than 1,000 views. For RNAseq sva-seq drops number of DE genes?
Popular Question 14 months ago, created a question with more than 1,000 views. For RNAseq sva-seq drops number of DE genes?
Popular Question 14 months ago, created a question with more than 1,000 views. For fastq parsing inefficiencies with python
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Scholar 2.6 years ago, created an answer that has been accepted. For A: Program for updating custom annotations with new genome?

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