User: mccormack

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mccormack30
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United States
Last seen:
7 months ago
Joined:
4 years, 11 months ago
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m********@molbio.mgh.harvard.edu

Posts by mccormack

<prev • 26 results • page 1 of 3 • next >
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Comment: C: How to extract bigWig signal for a given bed file?
... Great ! Thank you very much. Works very well. Numbers for all the ATGs (genes). ...
written 7 months ago by mccormack30
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Comment: C: How to extract bigWig signal for a given bed file?
... Hi Devon, Thank you very much for this script. I added three lines where you have the comment, 'Do something with the values': ATG = cols[3] # get the identifier from the bed file span = sum(vals) # sum all the values in vals print(ATG,"\t",span,"\n") This print ...
written 7 months ago by mccormack30
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Comment: C: DESeq2 results difference between use of lfcThreshold and sequential cutoffs.
... For Method A, the DESeq2 command is: res_WTK_WTN <- results(dds, contrast=c("condition", "WT-N", "WT-K")) The results of above are written into a tab-delimited .txt file and all genes with a FDR > 0.05 are removed. With the remaining genes, all genes with a log(2) of > 1 or < -1 a ...
written 13 months ago by mccormack30
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Comment: C: DESeq2 results difference between use of lfcThreshold and sequential cutoffs.
... I am not sure I understand. In my thinking, to take from your example in which all of the statistically significant genes (ssg), p-adj 0.05 or less, had a log(2) of between 1 and -1, then in Method A the ssg make it thru the initial FDR 0.05 cutoff while all the log(2) 1 genes are deleted in this st ...
written 13 months ago by mccormack30
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DESeq2 results difference between use of lfcThreshold and sequential cutoffs.
... I had been doing analysis using DESeq2 such that I would get the results from DESeq2, do a FDR (adj p-value) cutoff of 0.05 and then from that resulting list do a log(2) cutoff of greater than 1 and less than -1. I will call this Method A, 'sequential cutoffs' I have come to realize that the final ...
deseq2 written 13 months ago by mccormack30 • updated 13 months ago by cpad011211k
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RNA seq analysis when many genes are differentially expressed
... I know that many, if not all, differential expression analyses of RNA seq data assume that the majority of genes are not changing expression. However, what if you have data that when a FDR cutoff of 0.05 is used there are 30%, 40% or even 50% of genes are differentially expressed ? What distortion ...
deseq2 cuffdiff rna-seq edger written 16 months ago by mccormack30 • updated 16 months ago by Kevin Blighe46k
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Comment: C: HTSeq special counters occur at top and bottom of output file
... We could do this, but the HTSeq was fine for 16 of the 24 samples. It was only 8 samples that had this problem and I do not see any difference in the commands (other than file names) between samples that worked and samples that resulted in the special counters at the top and bottom of the output. ...
written 19 months ago by mccormack30
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Comment: C: HTSeq special counters occur at top and bottom of output file
... The BSUB -o command sends the output to the file named HTseq_S1_HTseq.txt. But, even if it were appending, why would it append only the special counters and not the count data ? ...
written 19 months ago by mccormack30
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Comment: A: HTSeq special counters occur at top and bottom of output file
... This is the command for S1. htseq-count -f bam --stranded=no /PHShome/data/HT/S1.bam /apps/lab/Brassica_napus.AST_PRJEB5043_v1.35.gtf ...
written 19 months ago by mccormack30 • updated 19 months ago by genomax70k
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HTSeq special counters occur at top and bottom of output file
... I have a bunch of HTSeq output files that have the special counters at the top and bottom of the file, and the numbers for each are different. For example, at the top of a file: __no_feature 5272304 __ambiguous 0 __too_low_aQual 0 __not_aligned 0 And, at the bottom of the file: ...
htseq written 19 months ago by mccormack30

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