User: berge2015

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berge201570
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Posts by berge2015

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Answer: A: extract or recode a gtf file based on a gene id list
... After playing with awk for a while, I came up with a solution: `awk -F'"' 'FNR==NR {block[$0];next} $2 in block' gene_id_list.txt ref_CDS.gtf > out.txt` [Note the quote delimeter] While not the most elegant solution, this does what's asked in the question. Hope it helps anyone else looking for s ...
written 6 weeks ago by berge201570
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extract or recode a gtf file based on a gene id list
... Hi, Does anyone here know how to extract lines from a gtf file using a list/subset of gene id obtained from the same gtf file? I basically want a 'recoded' (in vcf terminology) gtf file containing information for only those genes which I am interested in. I tried awk `awk 'FNR==NR {a[$0];next} {f ...
gene gtf rna-seq snp written 6 weeks ago by berge201570 • updated 6 weeks ago by shenwei3562.8k
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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 10 weeks 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 10 weeks ago by berge201570 • updated 10 weeks ago by EagleEye3.5k
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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 4 months 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 4 months 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 4 months 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 4 months 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 4 months 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 4 months ago by berge201570

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