User: apa@stowers

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apa@stowers320
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320
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Kansas City
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4 days, 15 hours ago
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4 years, 10 months ago
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a**@stowers.org

Posts by apa@stowers

<prev • 58 results • page 1 of 6 • next >
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Comment: C: tophat aligns to wrong strand
... When switching strands in the bam file, you would need to switch all strands, globally -- otherwise you are right, mate pairs would suddenly appear as discordant. IGV, in particular will color discordant pairs differently, but that is all. Other software may or may not pay attention to the concord ...
written 9 days ago by apa@stowers320
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Comment: C: tophat aligns to wrong strand
... > However, it's not correct that non-Tuxedo pipelines will read > alignments backwards. What I meant was that it reads the *correct* strand of the read backwards, sorry for my semantic glitch. The true strand of the RNA fragment is being reported wrong, because the library was made from rev- ...
written 10 days ago by apa@stowers320
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Comment: C: What is the difference between structural RNA-derived reads and non-structural R
... If anyone still does duplex-specific nuclease library normalization, it can have an effect too. It supposedly doesn't degrade sRNA species with hairpins or other secondary structure, but when we tried it, appeared to do it anyway. ...
written 10 days ago by apa@stowers320
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Comment: C: RPKM and FPKM directly comparable?
... You can convert them, in principle. The only difference between F and R is that F=R/N where N is the number of reads per fragment. So for single-end data, RPKM and FPKM are identical. For paired-end, FPKM = RPKM/2. In principle. If you used an FPKM estimator like Cufflinks or RSEM, then it will ...
written 10 days ago by apa@stowers320
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Comment: C: HT-seq Counts Very High Number of No Feature
... Ah hold on, I was only partially right. Even with "--library-type fr-firststrand" I think the strand will still be reversed in the bit flags. Tophat will just add the "XS" tag for strand -- which will contradict the bit flags -- but only Cufflinks reads this tag. Other software will still use the ...
written 10 days ago by apa@stowers320
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Answer: A: tophat aligns to wrong strand
... If I recall, use of "--library-type fr-firststrand" does not actually change the SAM bit flags. Instead, it adds the XS strand tag to the SAM record -- basically for Cufflinks to use. Non-Cufflinks programs will still read the alignments backwards. To really fix it, you'll need to edit the bit fl ...
written 10 days ago by apa@stowers320
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Answer: C: Error in read.table(file = file, header = header, sep = sep, quote = quote, :
... It is probably a problem with your header row. If the first row in the file has fewer fields than the second row, read.delim() (and all other functions built on it) will automatically assign column 1 to be rownames. ...
written 10 days ago by apa@stowers320
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Answer: A: Data resources for Chromatin accessibility (DNAse, FAIRE, ATAC - seq) and Transc
... You are basically looking for a public repository (google "sequencing public repository", for instance) Here are a few more big ones which handle next-gen sequencing data: - GEO ([https://www.ncbi.nlm.nih.gov/geo/][1]) - SRA ([https://www.ncbi.nlm.nih.gov/sra][2]) - ArrayExpress ([https://www. ...
written 10 days ago by apa@stowers320
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Comment: C: RNA contamination in WGS data
... That is correct as far as I know. ...
written 10 days ago by apa@stowers320
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Comment: C: How to convert bedgraph to bigwig?
... Go [here][1], choose your OS, and download all the Kent binaries you need. [1]: http://hgdownload.soe.ucsc.edu/admin/exe/ ...
written 10 days ago by apa@stowers320

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Scholar 12 days ago, created an answer that has been accepted. For A: lift coordinates mapping to_alt chromosomes in hg38
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