User: berge2015

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berge201570
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Posts by berge2015

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Comment: C: BWA mem running extremely slow
... After your suggestion (and reading your old post), I increased the memory to 32 GB and it still is as slow. I have decided for the time being to run multiple jobs in parallel to compensate for the slowness. While that's going, I will also play with increasing nodes, processors per node, memory, etc ...
written 5 days ago by berge201570
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Comment: C: BWA mem running extremely slow
... I too would like to put my money on the weirdness of the libraries leading to goofy fq files but really have not seen anything so out of the ordinary to notice it. What's insane is that I've done this numerous times in the past with species B but have never seen such slow output. My only solution t ...
written 5 days ago by berge201570
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Comment: C: BWA mem running extremely slow
... I do not think that's the issue. Maybe for the first file, yes, but not for all subsequent files. As I wrote above, each file is taking hours in my case. Besides, it runs pretty fast for the first species and I get 10-15 sam outputs for individuals from species A. ...
written 5 days ago by berge201570
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BWA mem running extremely slow
... An unusual problem regarding bwa alignment has been bugging me for about a week which I have not been able to troubleshoot. If anyone can help me resolve this, I'll ask Santa to get you 3 kegs of beer! I work with two plant species -- A & B -- and both have reference genomes. Ref seq sizes are ...
alignment sam bwa written 5 days ago by berge201570 • updated 5 days ago by Hussain Ather530
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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 9 months 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 9 months ago by berge201570 • updated 9 months ago by shenwei3563.4k
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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 months 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 months ago by berge201570 • updated 10 months ago by EagleEye4.8k
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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 12 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 12 months ago by berge201570

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