User: berge2015

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berge201570
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Posts by berge2015

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Comment: C: Plant KEGG pathway analysis in edgeR
... Wheat, but I'd like to use multiple plant species for my analysis. Arabidopsis, Rice, Maize, etc. ...
written 9 days ago by berge201570
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Plant KEGG pathway analysis in edgeR
... Hi, Does anyone know if there is a way to conduct KEGG pathway analysis in edgeR using the Plant database only? Or any other program, for that matter? When I use the `kegga` function, the results only have human KEGG IDs (hsa*). I however want to use only the information from plant species as I'm w ...
R kegg rna-seq written 9 days ago by berge201570 • updated 9 days ago by EagleEye3.2k
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Comment: C: How to call heterozygous SNPs
... If you are re-mapping the same reads, wouldn't any SNP you find technically be a het SNP? For example, if your assembly has a consensus base G at a locus but when you re-map the reads you find a G/A SNP at the same site, then this is a heterozygous site. Right? If no, please explain what your expect ...
written 11 weeks ago by berge201570
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Answer: A: qsub returns "no such file or directory error" for few files.
... If by 'PWD' you were directing your pbs script to your working directory, then that could be your problem. I personally prefer writing the full path, as in: `cd /home/user/your/working/directory/`) and it has always ran smoothly. Also, it's better to call the script as `perl script.pl` if the scrip ...
written 11 weeks ago by berge201570
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Comment: C: VCFtools alternative to --minDP flags not working?
... It may be worth trying an older version of vcftools, if that's a possibility. I just checked on version '0.1.12a' with `--minDP 1`, and it worked fine. ...
written 11 weeks ago by berge201570
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Comment: C: ERROR for Trinity abundance_estimates_to_matrix.pl
... It's safe to say that the issue is not with your perl script, but with edgeR. Most likely, you have missing values or NA in your file "Trinity_trans.TPM.not_cross_norm". Check if you do, and if yes, remove them and it should work. ...
written 11 weeks ago by berge201570
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Comment: C: Blastp e-value, bit score, identify importance to identify homolog sequences
... Depends on if you want an identical hit or similar-enough peptides. Whenever I've had to do this kind of work, I've always put more emphasis on columns 4 (Alignment length), 5 (Number of mismatches), and 6 (Number of gap opens) first. Because, as long as alignment length is 100% with 0 mismatch AND ...
written 11 weeks ago by berge201570
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Comment: C: how does cuffdiff treats replicates with high std?
... While I am not sure how exactly Cuffdiff treats replicates, you can use the flag `–max-bundle-frags` to skip overly abundant reads. You should be able to get a read count table from the bam file generated earlier to see what number you want to set as the cut-off threshold. ...
written 11 weeks ago by berge201570
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Answer: A: Filtering bed file
... try: `grep -v '^scaff*' infile > outfile` ...
written 11 weeks ago by berge201570
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Answer: A: How to construct a genetic map by association population ?
... If the lines are nicely related to each other (sibs, RILs, etc), you could try making pedigree-based map. If not, you'll have to align your sequences to the Glycine max genome to get the map for each line and other details. Then you can either merge the maps, or just use the sequence/marker order re ...
written 11 weeks ago by berge201570

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