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user790
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Posts by user

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Comment: C: interpreting minus strand reads in BAM?
... This says that it's the *leftmost* not rightmost:  "POS 1-based leftmost mapping POSition" https://www.projet-plume.org/files/sam1_v14.pdf   ...
written 4.2 years ago by user790
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Comment: C: interpreting minus strand reads in BAM?
... I just ran bedtools intersect on my BAM and the reads. the question is simply if a read aligns fully to minus strand annotation like chr1:24621346-24621401:-, do you ADD or SUBTRACT 50? assume read matches fully so no insertions/deletions. It sounds like you are saying you ADD 50, right? ...
written 4.2 years ago by user790
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interpreting minus strand reads in BAM?
... I have a 50bp long BAM read that aligns at start position 24621401 and it matches GFF interval "chr1:24621346-24621401:-". Does it mean the read starts at 24621401 and overlaps one base with the region? or is it within interval? do you subtract 50 or add 50 to the start position in this example? ...
next-gen alignment samtools rna-seq bam written 4.2 years ago by user790 • updated 4.2 years ago by Istvan Albert ♦♦ 78k
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Comment: C: Gene set enrichment tool for RNA-Seq in Python?
... which existing tools would you use, apart from GSEA? ...
written 4.6 years ago by user790
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linking ensembl gene ID to GO term?
... Is there a table that can be downloaded from FTP or accessed programmatically that links Ensembl ID for a given genome (like 'hg18' or 'mm9') to their GO terms - ids of the form "GO:..."? Is there a UCSC table that does this? I did not see any such table in: http://hgdownload.cse.ucsc.edu/goldenPath ...
ensembl gene-ids ucsc go gene-ontology written 4.6 years ago by user790 • updated 4.6 years ago by seidel6.6k
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Gene set enrichment tool for RNA-Seq in Python?
... Is there a library in Python for doing gene set enrichment analysis (GSEA, http://www.broadinstitute.org/gsea/index.jsp)? A library/tool that takes a foreground set of genes, a background set, a gene sets database like the one available from Broad and does the analysis without relying on microarray- ...
python gene-ontology go rna-seq gsea written 4.6 years ago by user790 • updated 2.7 years ago by Dataman260
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No PhyloP score for first stretch of chromosome?
... I'm looking at phyloP data from UCSC (http://hgdownload.cse.ucsc.edu/goldenPath/mm9/phyloP30way/vertebrate/). It looks like the first 3 million bases or so of some chromosomes don't have phyloP scores. Example:   $ zcat chr1.phyloP30way.wigFix.gz | head -n 5 fixedStep chrom=chr1 start=3000306 step ...
phylop alignment genome-browser ucsc written 4.7 years ago by user790 • updated 4.7 years ago by Alex Reynolds27k
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limit size of alignment generated by clustalw? Or related aligners?
... I am giving clustalw a set of sequences in FASTA format, each of length 5 (5 bases per sequence) using pretty much the default settings. Clustalw uses gaps in the resulting alignment and so the size of the resulting alignments can be quite long, e.g. 10 bases depending on size of the input. How can ...
fasta comparative-genomics alignment phylogenomics written 4.8 years ago by user790
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Gene Expression Signatures For Basal Vs Mesenchymal Breast Tumors?
... is there a canonical gene expression signature for a 'mesenchymal' breast tumor type versus a 'basal' breast tumor type? unsupervised gene expression clustering in primary breast tumors using PAM50 gene set often reveals five tumor subtypes (basal, her2, luminal a, luminal b and normal-like) but it' ...
clustering classification gene-expression genomics cancer written 4.8 years ago by user790 • updated 4.8 years ago by David Westergaard1.4k
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Comment: C: Trouble Compiling C++ Code With Bamtools
... I think the error might actually be that I passed bamtools-master/lib and not bamtools-master/src to the -L option of g++? ...
written 4.9 years ago by user790

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