User: Amitm

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Amitm1.4k
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Posts by Amitm

<prev • 188 results • page 1 of 19 • next >
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Answer: A: Mutations and copy number variations from DNA-Seq
... hi, You can perform CNV analysis using NGS data, provided the depth of coverage is sufficient. I think ~60x mean depth is decent for whole-exome. [This review][1] is a good starting point for choice of tools. A recent development is the use of off-target reads, along with on-target for better call ...
written 8 days ago by Amitm1.4k
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Comment: C: From TCGA to GDC (Genomic data commons)
... Nopes. I think that would be [GDC][1]. [1]: https://gdc-portal.nci.nih.gov/ ...
written 11 months ago by Amitm1.4k
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Comment: C: RepeatMasker: createLib() Error
... Not related to solving the error you are receiving.. It seemed from the input file specified in your cmd, that its a genomic fasta file. In that case, for many model organisms the location of repeats is available from [RepM][1] site as well as [UCSC Table Browser][2]. [1]: http://www.repeatmask ...
written 13 months ago by Amitm1.4k
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Comment: C: For RNA seq data analysis
... ![STAR param][1] Thats the way `--outReadsUnmapped` param is used. You have to say `Fastx` , and not an output file name. Refer to STAR manual plz [1]: https://s11.postimg.org/w1ip9f3jn/Screen_Shot_2016_11_18_at_23_25_30.png ...
written 14 months ago by Amitm1.4k
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Comment: C: STAR - genome indexes generation, genome file not created
... I haven't worked on the GRCh38 ver. of the genome. But by 'high car numbers' did you mean chr? Those are alt. contigs. and in case of GRCh37_primary_assembly there are >80. Here is the snippet of the log file, in case it helps - Finished loading and checking parameters Mar 25 21:46:26 .. ...
written 14 months ago by Amitm1.4k
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Comment: C: STAR - genome indexes generation, genome file not created
... STAR needs about ~30Gb of RAM for human genome. Did you ensure that sufficient RAM was available? How long did you wait? With GRCh37 (Ensembl fasta and GTF) and 8 threads and 40Gb RAM, it took me ~50mins to generate the index. ...
written 14 months ago by Amitm1.4k
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Answer: A: How to annotate CNV events with gene information?
... hi, A float of 0.5 passed to `-f` seems reasonable, in intersectBed. Once happy with threshold, make a shell script like this - bedtools2-2.20.1/bin/intersectBed \ -a "$1" \ -b Homo_sapiens.GRCh37_BED_SORTD.txt \ -wao \ -f 0.5 \ >"$1"_ANNO And save it in a file, say CNV ...
written 14 months ago by Amitm1.4k
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Comment: C: For RNA seq data analysis
... Have a look here - https://www.biostars.org/p/157705/ and specifically for getting reads that do not align, use the `--outReadsUnmapped` parameter if you use [STAR][1]. [1]: https://github.com/alexdobin/STAR ...
written 14 months ago by Amitm1.4k
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Comment: C: Somatic mutations from RNA-Seq data of tumor vs. normal
... hi, This is what I did for filtering the calls from RNA-seq. First annotate the calls with the read depth info. (no. of reads supporting the variant & ref. allele). Then if you look at the read depth for the var. allele, you would see most have ~2 supporting reads only. Caveat - This is what I ...
written 14 months ago by Amitm1.4k
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Comment: C: viewing microRNA in IGV
... The usual genome should work. I am assuming that the alignment (for the small RNA-seq reads) was done on hg19 genome. ...
written 15 months ago by Amitm1.4k

Latest awards to Amitm

Scholar 8 days ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Appreciated 4 months ago, created a post with more than 5 votes. For A: Kmer Content in FastQC failed
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Kmer Content in FastQC failed
Popular Question 5 months ago, created a question with more than 1,000 views. For Removing PCR primers in targeted sequencing with nested amplicons
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Scholar 8 months ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Kmer Content in FastQC failed
Scholar 15 months ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Scholar 16 months ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Appreciated 16 months ago, created a post with more than 5 votes. For A: Kmer Content in FastQC failed
Guru 16 months ago, received more than 100 upvotes.
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Commentator 18 months ago, created a comment with at least 3 up-votes. For C: Assemble fully overlapping reads into contigs that may have several clones
Voter 20 months ago, voted more than 100 times.
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Centurion 22 months ago, created 100 posts.
Commentator 23 months ago, created a comment with at least 3 up-votes. For C: Assemble fully overlapping reads into contigs that may have several clones
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Scholar 24 months ago, created an answer that has been accepted. For A: Somatic allele frequency from TCGA
Supporter 2.0 years ago, voted at least 25 times.
Commentator 2.0 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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