User: cpad0112

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Posts by cpad0112

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Comment: C: How to Interpret COSMIC/HGVS Gene Fusion Format
... AKAP9{ENST00000356239}:r.1_3551+364_BRAF{ENST00000288602}:r.1202-1794_2480 Fusion event involves: 1. AKAP9 transcript. Exon 1 (1-3551) + intron (364bp downstream of exon 1) 2. BRAF transcript : transcript bases starting from intron (1202bp) upstream of exon (spanning1202-1794) till the e ...
written 11 hours ago by cpad01121.7k
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Comment: C: Average intron length in Drosophila melagnoster
... with [seqkit:][1] seqkit stats dmel-all-intron-r6.16.fasta.gz output: file format type num_seqs sum_len min_len avg_len max_len ../example_data/dmel-all-intron-r6.16.fasta.gz FASTA DNA 71,654 117,455,516 2 1,639.2 ...
written 1 day ago by cpad01121.7k
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Comment: C: Average intron length in Drosophila melagnoster
... withou awk: zgrep \> dmel-all-intron-r6.16.fasta.gz | cut -d '=' -f8 | tr -d ' ;' | datamash -s mean 1 median 1 ...
written 1 day ago by cpad01121.7k
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Answer: C: Average intron length in Drosophila melagnoster
... Download intron fasta file from ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/fasta/dmel-all-intron-r6.16.fasta.gz, as posted by Alex Reynolds and run following command: zgrep \> dmel-all-intron-r6.16.fasta.gz | awk -F '[;=]' '{print $14}' | datamash mean 1 median 1 o ...
written 1 day ago by cpad01121.7k
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Comment: C: bioawk output in original fastq format
... refer to post on searching fastq files: https://www.biostars.org/p/138643/ ...
written 1 day ago by cpad01121.7k
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Comment: C: Question about ifelse in R
... did you the check the class of variables that you are passing to pf? ...
written 2 days ago by cpad01121.7k
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Comment: C: Any great tutorials on how to download sift/provean on your computer?
... If you are using ubuntu or mint, try sudo apt-get install sift -y Enable universe, multiverse, restricted repos and update the repos before you install sift, to be on safe side. Xenial (ubuntu) and Sonya (mint) have sift in their repos. Current version in repos is 4.0.3b ...
written 3 days ago by cpad01121.7k
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Comment: C: Locating longest gene, CDS in Ensembl GTF
... Yes. Further even, awk is not necessary as it is extracting all rows with word "exon" in it and zgrep can do it.. A shorter code is as below compared to code posted above: ( I am not sure if it is any faster): Code pasted from above (except for input): $ gunzip -c Homo_sapiens.GRCh38.86.gtf.g ...
written 4 days ago by cpad01121.7k
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Comment: C: Find number of X and Y chromosomes in each sample (.csv data)
... grep the file by chromosome x and y. Please post few example lines here ...
written 4 days ago by cpad01121.7k
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Comment: C: Locating longest gene, CDS in Ensembl GTF
... grep -v is not necessary. ...
written 4 days ago by cpad01121.7k

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Commentator 5 days ago, created a comment with at least 3 up-votes. For C: Problem installing Rgraphviz in R
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Scholar 22 months ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
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Scholar 22 months ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Scholar 22 months ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Scholar 22 months ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps

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