User: newbio17
newbio17 • 320
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Posts by newbio17
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... MBASED can generate gene-level ASE with/without phasing information ([paper][1], [R package][2]).
[1]: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0405-3
[2]: https://bioconductor.org/packages/release/bioc/html/MBASED.html ...
written 5 days ago by
newbio17 • 320
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... I think you should check out [miRWalk][1].
[1]: http://mirwalk.umm.uni-heidelberg.de/ ...
written 5 days ago by
newbio17 • 320
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... You may want to try hisat2 if you don't have access to a machine/server with the minimum memory requirement (generally, people seem to report better performance from STAR). Depending on your needs, you may also want to look into kallisto/salmon for pseudo-alignments. ...
written 8 days ago by
newbio17 • 320
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Comment:
C: Help Compiling STAR
... You can also try installing via conda to resolve dependencies: `conda install -c bioconda star` ...
written 12 days ago by
newbio17 • 320
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... You can use tcgabiolinks to look up clinical information: [TCGAbiolinks: Clinical data][1]
[1]: https://bioc.ism.ac.jp/packages/3.7/bioc/vignettes/TCGAbiolinks/inst/doc/clinical.html ...
written 5 weeks ago by
newbio17 • 320
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Comment:
C: TCGA BRCA data composition
... Clinical and biomedical data for TCGA-BRCA show stage, subtype, ethnicity, country of origin (and more, if you need), all of which you might want to reference before using the data from 2 publications as independent cohorts. ...
written 6 weeks ago by
newbio17 • 320
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C: Variant Calling - Ion Torrent
... Ion Torrent workflow is a bit unconventional compared to what you're probably used to with Illumina data. When I had to deal with such data in the past, I found some help in a previous Biostars post [here][1], specifically the part where it talks about how `.bam` files generated from Ion Torrent sto ...
written 7 weeks ago by
newbio17 • 320
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... If 52% of the reads are aligning to regions other than CDS-Exons, especially introns, then I would suspect there may be DNA contamination. Most of the downstream analyses should be okay assuming you have enough reads mapped to CDS-Exons.
Considering that you have RNA-Seq data, I would say it's not ...
written 7 weeks ago by
newbio17 • 320
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... 60% unassigned/multi-mapped reads is a little high. You can try to check for DNA contamination with `read_distribution.py` from RSeQC (more hits in non-coding regions if present). ...
written 8 weeks ago by
newbio17 • 320
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Comment:
C: genome coverage visualization
... You can try to divide and compute mean coverage for regions instead of trying to visualize individual positions. You can find some other ideas [here][1].
[1]: https://girke.bioinformatics.ucr.edu/GEN242/mydoc_Rgraphics_7.html ...
written 8 weeks ago by
newbio17 • 320
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