User: tiago211287
tiago211287 • 940
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Posts by tiago211287
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... Actually, there is, using max-procs 1, you avoid loops. ...
written 3 months ago by
tiago211287 • 940
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... Are you doing synteny analysis? ...
written 3 months ago by
tiago211287 • 940
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... What is your RNA-seq material, and What is the reference genome are you using ? ...
written 3 months ago by
tiago211287 • 940
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... Tip: When posting code, use the code sample button to make it easier to read.
"EOF marker is absent" means that your BAM file has been truncated. Did Tophat produce a BAM or a SAM file? How did you convert from sam to bam? ...
written 3 months ago by
tiago211287 • 940
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... This task can be accomplished with [FASTA/Q Collapser][1] quickly.
[1]: http://hannonlab.cshl.edu/fastx_toolkit/commandline.html ...
written 3 months ago by
tiago211287 • 940
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... Here is a little tip for your volcano plot:
Make a column with information about who is DEG, and who is not
DESeq.Result$super <- DESeq.Result$log2FoldChange > 1 & DESeq.Result$padj < 0.01
DESeq.Result$sub <- DESeq.Result$log2FoldChange < -1 & DESeq.Result$padj & ...
written 3 months ago by
tiago211287 • 940
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... You are totally right. I made it myself when I was learning.
A way of using without upsetting coworkers is limit the network band with less or equal to 50 Mbps "-l50m" and always set the --maxprocs parameter in parallel to a low value.
Talk with the admin is a good idea.
...
written 3 months ago by
tiago211287 • 940
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... > As the sizes of the datasets have increased, we have found that the
> traditional methods of FTP or HTTP do not have the performance
> characteristics needed to support this load of data. FTP performance
> degrades proportionally with the number of hops or switches the data
> must t ...
written 3 months ago by
tiago211287 • 940
• updated
3 months ago by
genomax ♦ 47k
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... Count the number of sequences in 1 fasta file:
grep -c ">" file.fasta
Count the number of sequences in several fasta files:
find /home/folder/to/file/ -name "*.fasta" | parallel grep -Hc ">" {}
Get the length of each instance of a fasta file:
grep -v ">" 180110.fasta | awk ...
written 3 months ago by
tiago211287 • 940
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... It depends on your target organism and tissue. Also, adjusted p-values(padj) of 0.1 aren't big. 0.1 = 10%. In general, a good cutoff for considering a gene as a DEG is less than 0.01 (1%).
Better to visualize it in the minus (-log10(padj)) scale so that anything between 0 and 1 will be a non-DEG, a ...
written 3 months ago by
tiago211287 • 940
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