User: newbio17

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newbio17320
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Posts by newbio17

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Comment: A: allele specific expression at gene level
... 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 newbio17320
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Comment: C: miRanda - is it still up and running?
... I think you should check out [miRWalk][1]. [1]: http://mirwalk.umm.uni-heidelberg.de/ ...
written 5 days ago by newbio17320
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Comment: C: Any idea on how long fastq mapping takes in STAR?
... 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 newbio17320
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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 newbio17320
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Comment: C: Paired Tumor and Normal Sample for BRCA-Subtype
... 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 newbio17320
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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 newbio17320
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Comment: 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 newbio17320
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Comment: C: High mapping on chromosome M in RNA-seq data
... 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 newbio17320
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Comment: C: High mapping on chromosome M in RNA-seq data
... 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 newbio17320
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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 newbio17320

Latest awards to newbio17

Popular Question 5 weeks ago, created a question with more than 1,000 views. For Detecting antisense RNA in unstranded RNA-Seq data
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Regions & Covered BED files for Agilent SureSelect All Exons v2
Scholar 5 months ago, created an answer that has been accepted. For A: Looking for dbSNP b144 version vcf
Supporter 5 months ago, voted at least 25 times.
Popular Question 6 months ago, created a question with more than 1,000 views. For Appending sequence decoys and virus sequences to reference genome (GRCh38)
Popular Question 9 months ago, created a question with more than 1,000 views. For Orientation of reads in .fastq files from RNA-Seq
Popular Question 10 months ago, created a question with more than 1,000 views. For Orientation of reads in .fastq files from RNA-Seq
Scholar 11 months ago, created an answer that has been accepted. For A: Looking for dbSNP b144 version vcf
Scholar 11 months ago, created an answer that has been accepted. For A: Looking for dbSNP b144 version vcf

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