User: Longshotx

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Longshotx 20
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Posts by Longshotx

<prev • 31 results • page 1 of 4 • next >
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Help with Hmmscan
... How can I tell hmmscan to take the top scoring target and output that instead of querying each contig node against the hmm profile database? I created a hmm profile using the 735 BacMet v2 experimentally confirmed protein database using jackhmmer against the 151k protein homologs. I built a hmm pro ...
alignment metagenome hmmscan blast hmmer written 9 weeks ago by Longshotx 20
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Comment: C: Using blast or similar tool to annotate ORFs using Bacmet database
... Hi again Mensur So I hope I am setting this up correctly because I just ran it using parallel and it finished without any output file. So I have a directory with a .fasta for everyone of the 735 genes and the database containing the 155k genes is in a directory above. I ran this command: ls ...
written 10 weeks ago by Longshotx 20
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Comment: C: Using blast or similar tool to annotate ORFs using Bacmet database
... Excellent thank you. I'm going to try the BacMet 735 experimentally confirmed genes against the against BacMet predicted database of 155k gene homologs for now. ...
written 10 weeks ago by Longshotx 20
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Comment: C: Using blast or similar tool to annotate ORFs using Bacmet database
... I have never used either of those tools, but it appears I can use the jackhmmer script on the cluster I am working on. Could you suggest a db to use? I am assuming nr? Or I could use the BacMet predicted genes as a database...that has 150,000 genes. ...
written 10 weeks ago by Longshotx 20
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Comment: C: Using blast or similar tool to annotate ORFs using Bacmet database
... I tried to do something similar to the hmm profile strategy but got confused. I originally aligned all the the proteins in Bacmet and build a hmm profile, but when I performed a search the query said "Bacmet alignment" for all of them which is not helpful at all. Are you suggesting I build a hmmprof ...
written 10 weeks ago by Longshotx 20
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Using blast or similar tool to annotate ORFs using Bacmet database
... Hello all - I am interested in annotating some ORFs I assembled using the 753 experimentally confirmed genes in Bacmet (http://bacmet.biomedicine.gu.se/) as a reference. Basically I want to do a blast search against this database and annotate similarly matched ORFs if they have an evalue less than o ...
annotation alignment metagenome prodigal written 10 weeks ago by Longshotx 20 • updated 10 weeks ago by Mensur Dlakic2.1k
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Trying to find best way to determine co-occurence between taxa and genes related to antibiotic resistance.
... Hi thanks for reviewing my question. I have some metagenomic datasets, four sample groups that I used to predicted ORFs containing antibiotic resistance. I mapped the reads back to the ORFs and used a formula to get the transcripts per million (TPM) for each ORF. I then annotated these ORFs against ...
R co-occurence cytoscape statistics written 11 weeks ago by Longshotx 20
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Comment: C: How to run several one-way ANOVAs in R using on different categories?
... Thanks this was extremely helpful! ...
written 11 weeks ago by Longshotx 20
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Comment: C: Predicted Proteins: Mapping Reads to ORFs
... Thank you! That was very helpful. ...
written 11 weeks ago by Longshotx 20
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Comment: C: Get genes and coverage/depth per gene from sam/bam
... Any luck with this @prishly? ...
written 3 months ago by Longshotx 20

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