User: yarmda

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yarmda0
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Posts by yarmda

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Comment: C: biopython esearch not giving all children taxIDs
... Actually, I think it may have been an issue with a default retmax of 20. ...
written 21 hours ago by yarmda0
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biopython esearch not giving all children taxIDs
... I know similar questions have been posted before.. https://www.biostars.org/p/58955/ https://www.biostars.org/p/17715/#273935 But, I am having trouble retrieving the children sequences of a given taxID. For instance, from Bio import Entrez record = Entrez.read(Entrez.esearch(db='protein ...
ncbi biopython entrez written 1 day ago by yarmda0 • updated 17 hours ago by Renesh910
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Comment: C: Refseq Proteins For A Given Taxid
... I don't know if this will still get any attention, but I am running into RuntimeError: Search Backend failed: or no elements found. Any thoughts? I've gotten around this by not using so many variables. It's a little less clean, but it works. ...
written 1 day ago by yarmda0
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Comment: C: Command line to download fasta sequences from PATRIC DB
... These files seem to have fewer proteins than were indicated by the protein families page for a given strain. That may be fine, but can you explain why? For instance, genome 1392.82 has a protein families page that would have 5400 or so sequences, while the file from the ftp stops around 4500 or so. ...
written 10 days ago by yarmda0
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Comment: C: Command line to download fasta sequences from PATRIC DB
... That downloads the table. I want the fasta sequences. That is also not a command line option that would be scalable to an arbitrary number of organisms and their strains. ...
written 10 days ago by yarmda0
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Command line to download fasta sequences from PATRIC DB
... I am seeking to download every available protein sequence for a series of organisms and all of their strains. PATRIC offers more strains than NCBI has listed (as far as I can tell, feel free to correct that and please indicate how I can find the corresponding sequences on NCBI), but I can't tell how ...
command patric download written 10 days ago by yarmda0
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Comment: C: How to generate a multiple HMM file with HMMER?
... SELEX approximates the Stockholm format used by pfam http://www.csb.yale.edu/userguides/seq/hmmer/docs/node30.html ...
written 3 months ago by yarmda0
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How to generate a multiple HMM file with HMMER?
... I want to generate a file that contains multiple HMMs, one each for given genes. HMMER documentation says this can be done, if created from a file containing more than one multiple sequence alignments. Further in HMMER docs, it says that a multiple MSA file must be in "Stockholm format," as the writ ...
hmmer stockholm msa written 3 months ago by yarmda0 • updated 3 months ago by Sej Modha1.8k
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Comment: C: How to extract only continuously aligned reads from a SAMfile
... The solution is listed as samtools view -f 256 Input.bam | awk '$6 ~/S/ && $7 == "=" {print $0}' > Secondary_clipped.sam But, this pulls out secondary alignments and then checks if there is a soft clipping event. Secondary alignments may happen, but this won't necessarily capture all c ...
written 5 months ago by yarmda0
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Comment: C: How to extract only continuously aligned reads from a SAMfile
... We are considering that option, but that still leaves a risk of chimeric reads being included, depending on how the trimming worked out. We're hoping to be able to identify about 30-40% of the reads as non-chimeric. If we can't identify even 15% as non-chimeric, we'll probably resort to trimming. ...
written 5 months ago by yarmda0

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Supporter 5 months ago, voted at least 25 times.

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