User: cpad0112
cpad0112 • 1.7k
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Posts by cpad0112
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... 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
cpad0112 • 1.7k
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... 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
cpad0112 • 1.7k
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... 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
cpad0112 • 1.7k
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... 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
cpad0112 • 1.7k
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... refer to post on searching fastq files: https://www.biostars.org/p/138643/ ...
written 1 day ago by
cpad0112 • 1.7k
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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
cpad0112 • 1.7k
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2
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148
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... 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
cpad0112 • 1.7k
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... 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
cpad0112 • 1.7k
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... grep the file by chromosome x and y. Please post few example lines here ...
written 4 days ago by
cpad0112 • 1.7k
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204
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2
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... grep -v is not necessary. ...
written 4 days ago by
cpad0112 • 1.7k
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