User: mforde84

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Posts by mforde84

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Comment: C: How to filter normalized RNA-Seq transcripts for the purpose of predicting a con
... General speaking I'd filter all genes with 0 sum counts, and average CPM/TPM/RPKM/FPKM less than 1. Then normalize filtered counts for library size and between subject variance. Limma voom is very good for this application and can incorporate quality weights for sequencing libraries. Then for regres ...
written 5 months ago by mforde841.2k
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Job: Bioinformatics role becoming available at University of Chicago
... Hi everyone, I'm transitioning to a new role at the University of Chicago, and looking to help find a replacement for my bioinformatics position within the Department of Radiation Oncology. We work primarily with clinical sequencing and microarray of patient samples, immortalized cell lines, and xe ...
genome ngs microarray job written 7 months ago by mforde841.2k • updated 6 months ago by ankur.chaturvedi1719870
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Comment: C: How to select tumor GO terms, if I did not find any in my biological process GO
... There's a lot of biological processes implicated in tumor biology. GO isn't really going to tell you which ones are tumor biology or not (except in a small number of situations). You need to be familiar with the literature and understand which biological processes are implicated in tumor biology, as ...
written 8 months ago by mforde841.2k
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Comment: C: Merge fastq reads for several samples
... maybe im just being too literal here, but he seems to be saying that he's merging reads from two independent runs. and if thats the case, then he probably should be treating each run as a technical replicate, or consider merging after correcting for batch effects. ...
written 8 months ago by mforde841.2k
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Comment: C: rsem-calculate-expression fails to open iso_res file
... look at the permissions of the folder in question. check that it's readable, and writable to the user running the process 'ls -l'. check that you have available space on the mount point 'df -h'. if all else fails, delete the temporary folders and files associated with the RSEM analysis, and rerun ...
written 8 months ago by mforde841.2k
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Comment: C: How to select tumor GO terms, if I did not find any in my biological process GO
... If a term isn't enriched, then it's not enriched. An unbiased and data driven analysis is much more valuable then massaging your data over and over to eventually come to a result you expected. You might be better off looking at go terms directly associated with "tumor". There's not many (~90 or so) ...
written 8 months ago by mforde841.2k
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Comment: C: Fundamental Analysis of TCGA RNA-seq Data-01
... what ... exactly ... do ... you ... want? ...
written 8 months ago by mforde841.2k
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Comment: C: Merge fastq reads for several samples
... Why are you merging reads again? ...
written 8 months ago by mforde841.2k
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Comment: C: WES -- How come I found 40% mutations intron regions
... This would filter out all reads mapping to intronic regions prior to base score recalibration and variant calling based upon genomic intervals annotated as exonic in the assemblies corresponding gtf or gff file. Might actually be the best way to do it, IMO. awk ' $3 == "exon" ' Homo_sapiens.GRC ...
written 8 months ago by mforde841.2k
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Comment: C: rsem-calculate-expression fails to open iso_res file
... sounds like a permissions issue. why are you running as root? ...
written 8 months ago by mforde841.2k

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