User: Amitm

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Amitm1.6k
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Posts by Amitm

<prev • 223 results • page 1 of 23 • next >
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Comment: C: faster variant annotation for large VCFs
... Hi, Have you been able to make it work? After installing VEP, you need to have run - perl \ INSTALL.pl \ --AUTO p \ --PLUGINS CADD,ExAC \ --SPECIES homo_sapiens_merged \ --ASSEMBLY GRCh37 That would configure the plugins (you specify) under the vep data cache Plugins/ path. ...
written 1 day ago by Amitm1.6k
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Comment: C: faster variant annotation for large VCFs
... many thanks! Going to try this ...
written 13 days ago by Amitm1.6k
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faster variant annotation for large VCFs
... hi there, I am trying to annotate WGS VCF files through VEP, and even on multi-threading (n=8) the process is painfully slow. The VCF sizes range between 1-1.5Gb. Around 2 days for each VCF What would you recommend to speed up the process? I can break the VCF into chunks. Any other sol. or softwar ...
vcf wgs variant annotation written 13 days ago by Amitm1.6k • updated 13 days ago by Emily_Ensembl15k
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Comment: C: Removing everything after the last underscore in the header of a fastafile
... sorry, I think this is not removing stuff from the last '_' onwards, but just printing the 1st four '_' sep values. ...
written 13 days ago by Amitm1.6k
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Answer: A: Removing everything after the last underscore in the header of a fastafile
... Hi, This should work - awk -F '_' '{if (/^>/) print $1"_"$2"_"$3"_"$4; else print $0;}' test.fasta ...
written 13 days ago by Amitm1.6k
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Comment: C: GISTIC input parameters.
... Hi, Did you provide the 'control' CNV data using the `-cnv` param? That param can be used provide segments that are seen in healthy pop. and/ or control samples. The GISTIC repo. has a file provided for that param, under here - ftp://ftp.broadinstitute.org/pub/GISTIC2.0/hg19_support/ Pick the file ...
written 15 days ago by Amitm1.6k
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Comment: C: Error : run cnvkit from bam
... If it helps, I used the set-up below and it did work fine. cnvkit.py batch \ BAM_files /path/to/tumour/*.bam \ --normal /path/to/germline/*.bam \ --drop-low-coverage \ -p 12 \ --targets my_CNVKit_Targets_AutosomesOnly.bed \ --antitargets my_CNVKit_AntiTargets.bed \ - ...
written 15 days ago by Amitm1.6k
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Comment: C: Error : run cnvkit from bam
... Hi, There seems to be an additional space after the `-r` argument. Can you remove the extra space and run again. Not sure though if this is the main reason, but try ...
written 15 days ago by Amitm1.6k
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Comment: C: Error : run cnvkit from bam
... Hi, If you post the cmd you actually ran, that might be more helpful in finding what might be wrong. ...
written 15 days ago by Amitm1.6k
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Answer: A: Different results for differentially expressed genes in RNA-seq analysis with cu
... Hi, Are you sure you are working with FPKM values? If yes, then such data is not amenable to t-test (or similars), because FPKM data can't be approximated by Normal distribution (which is required for variants of t-test). And thats the reason, cuffdiff used beta-negative binomial distribution. Coun ...
written 19 days ago by Amitm1.6k

Latest awards to Amitm

Appreciated 6 weeks ago, created a post with more than 5 votes. For A: Kmer Content in FastQC failed
Scholar 6 weeks ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Scholar 6 months ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Scholar 8 months ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Appreciated 13 months ago, created a post with more than 5 votes. For A: Kmer Content in FastQC failed
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: Kmer Content in FastQC failed
Popular Question 14 months ago, created a question with more than 1,000 views. For Removing PCR primers in targeted sequencing with nested amplicons
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Scholar 17 months ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Good Answer 18 months ago, created an answer that was upvoted at least 5 times. For A: Kmer Content in FastQC failed
Scholar 24 months ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Scholar 2.0 years ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Appreciated 2.1 years ago, created a post with more than 5 votes. For A: Kmer Content in FastQC failed
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Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Commentator 2.2 years ago, created a comment with at least 3 up-votes. For C: Assemble fully overlapping reads into contigs that may have several clones
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Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
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Commentator 2.6 years ago, created a comment with at least 3 up-votes. For C: Assemble fully overlapping reads into contigs that may have several clones
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Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA

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