User: tiago211287
tiago211287 • 990
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Posts by tiago211287
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Comment:
C: bam file merge
... In http://www.htslib.org/doc/samtools-1.2.html,
it says,
> -h is specified the @SQ headers of input files will be merged into
> the specified header, otherwise they will be merged into a composite
> header created from the input headers. If in the process of merging
> @SQ lines for coor ...
written 19 days ago by
tiago211287 • 990
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Comment:
C: Filtering rRNA from RNAseq data
... You can normally align the reads against genome + annotation (gencode), using STAR for example which can count the number of reads/feature. Then just check the annotated rRNA gene count percentage. You would need "good" samples as a control of what is normal/bad. ...
written 4 weeks ago by
tiago211287 • 990
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... Have you already called your peaks? You can Use MACS2 for peak calling. To only then, choose strong peak signals. I would also use deeptools to access Chip-Seq Sequencing quality and statistics. ...
written 4 weeks ago by
tiago211287 • 990
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... Actually, there is, using max-procs 1, you avoid loops. ...
written 5 months ago by
tiago211287 • 990
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... Are you doing synteny analysis? ...
written 5 months ago by
tiago211287 • 990
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... What is your RNA-seq material, and What is the reference genome are you using ? ...
written 5 months ago by
tiago211287 • 990
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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 5 months ago by
tiago211287 • 990
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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 5 months ago by
tiago211287 • 990
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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 5 months ago by
tiago211287 • 990
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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 5 months ago by
tiago211287 • 990
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