Activity for Peter Bazeley
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Peter Bazeley posted a comment on ticket #80
Hi Adam, As the author pointed it was a Perl issue. I installed MOCAT with another account and had no issues. So I would talk to your admin about having the correct version of Perl in your PATH, and use that edit as a last resort. Also the lack of indentation is just my laziness... -Peter
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Hi. So in my quest to find abundances for the FMGs in each sample, it appears that there's no good way to associate COGs with the IGC catalog (or is there?). So the alternative appears to be to take the gene.prediction.assembly result sequences, extract the ones that were matched with the FMGs, and align those to the IGC catalog. Does that sound reasonable? Thanks, Peter
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Not for taxanomic comparison but as a way to deal with compositional bias. Wouldn't this give a kind of average gene abundane per species, or am I way off?
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Abundance scaled by FMG abundances?
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Do you have more details of how this is calculated? Is it just a proportion of the gene length that has any read alignment or is it weighted by the number of reads? I'm wondering how to interpret these. Thanks. On Mon, Feb 12, 2018 at 4:21 AM, MOCAT <mocat-pipeline@users.sourceforge.net wrote: No. These are the horizontal gene coverages (what fraction of the gene has coverage), which is not related of horizontal gene transfers. On Mon, Feb 12, 2018 at 05:25 Peter Bazeley theoark@users.sourceforge.net...
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Genome size normalization?
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horizontal gene coverage
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Hi, I ended up just commenting out line 51, and changing line 56 to: " my @line_parts = scalar @line; my @cogs; if (defined($line[$i])) { @cogs = split /[,|]/, $line[$i]; } else { @cogs = '' x $line_parts; } " and this runs fine. HTH, Peter
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Functional.pm line 51: "Modification of read-only value attempted"
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I downloaded the IGC.zip file from the MOCAT website, unzipped it, and when I try: MOCAT.pl -sf my.samples -s IGC -screened_files I get: Mon Jan 8 09:35:30 2018: PERFORMING SCREEN USING DATABASE... Mon Jan 8 09:35:30 2018: Checking files... OK! Mon Jan 8 09:35:30 2018: Creating screen jobs... ERROR & EXIT: IGC is not a valid database path at <mocat dir="">/src/MOCATScreen.pm line 134. It works if I copy the map files to IGC.1.functional.map and use: MOCAT.pl -sf my.samples -s IGC.1 -screened_files...
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IGC.1 and IGC.2
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Thanks, this solved the issue. Appreciate your help.
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Hello, To piggy-back off of this ticket, if I want to do the above but also filter against hg19 prior to IGC, would I use the following commands: MOCAT.pl -sf my.samples -rtf MOCAT.pl -sf my.samples -s hg19 MOCAT.pl -sf my.samples -s IGC -r hg19 MOCAT.pl -sf my.samples -f IGC MOCAT.pl -sf my.samples -p IGC -mode functional Thank you for your assistance, Peter
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Or should I convert to this format: @HWUSI-EAS100R:6:73:941:1973#0/1
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My headers (1 from each PE file) looks like this: @K00136:435:HGL7GBBXX:4:1104:16985:30433 1:N:0 @K00136:435:HGL7GBBXX:4:1104:16985:30433 2:N:0 This looks similar to the wikipedia page for Casava 1.8: " With Casava 1.8 the format of the '@' line has changed: @EAS139:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG " except no index sequence at the end. Should I add a dummy sequence at the end? Thanks for your help, Peter
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RTF Saving PE reads as single FQ
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