User: mss

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mss30
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1 month, 3 weeks ago
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2 years, 2 months ago
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m*****@islander.tamucc.edu

Posts by mss

<prev • 55 results • page 1 of 6 • next >
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Counting Genomes from NCBI and GOLD
... Hi, I am trying to find the best and easiest way to get counts of SAGs, MAGs, and isolate genomes for each bacterial phylum from either NCBI or GOLD. I wish these databases made the numbers easily accessible like [IMG][1]. I first used NCBI's E-utilities to search for assemblies "derived from me ...
genome ncbi gold metagenome single cell written 8 weeks ago by mss30
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Comment: C: Diploid genome gene annotation
... Update: I decided to go forward with the haploid genomes instead, so I used [purge_haplotigs][1] pipeline to do so. The genomes were greatly reduced in size and annotations. [1]: https://bitbucket.org/mroachawri/purge_haplotigs/src/master/ ...
written 10 weeks ago by mss30
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Comment: C: Understanding the gffcompare output for my dataset
... Sorry, I know it has been a long time since this was posted, but I also have low precision values and I am wondering if you found out why that is? ...
written 6 months ago by mss30
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Subset Function in Ballgown
... Hello, I am using the HISAT, Stringtie, and Ballgown pipeline to do transcriptome expression analysis. So far I went through these steps. bg=ballgown(dataDir=data_directory, samplePattern='1and2', meas='all') bg_ifungis = ballgown(dataDir = data_directory, samplePattern = '1and2', pDat ...
differential expression transcriptome written 6 months ago by mss30 • updated 6 months ago by Amar650
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Comment: C: Redirecting pHMMER output to /dev/null
... I don't have much experience in using programming languages to create scripts, but I will see what I can find. Thanks for the advice! ...
written 13 months ago by mss30
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Comment: C: Redirecting pHMMER output to /dev/null
... The developer of hmmer recommended that I use head -4 in conjunction with /dev/null. Unfortunately, what I need is just the top hit per-query basis and I don't have the skills to create a script to do this. I wonder why hmmer does not have the option to output just one hit per a query like blast al ...
written 13 months ago by mss30
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Comment: C: Redirecting pHMMER output to /dev/null
... I edited my original question with what the tbl file looks like in Excel. I want one hit for each gene, but instead I am getting several 100 to 1000 hits for each query. ...
written 13 months ago by mss30
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Comment: C: Redirecting pHMMER output to /dev/null
... Unfortunately, it did not work. My tbl output still looks the same. :/ I am kind of at a lost... ...
written 13 months ago by mss30
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Comment: C: Redirecting pHMMER output to /dev/null
... Yes, I thought that the .tbl and the output were the same file since I was using --tblout . That is correct, I wanted the results file to only include the top hit from each gene. When I was contacting the developer, what he said/what I understood was to discard the main output to /dev/null, save a ...
written 14 months ago by mss30
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Comment: C: Redirecting pHMMER output to /dev/null
... Thanks for your help, I understand now what you are saying about the differences in stdout and stderr but how does this script only give me the top hit for each of my queries? Wouldn't I need to add something like head -4, to tell it to throw everything out of the stderr that isn't the top hit? Whe ...
written 14 months ago by mss30

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Popular Question 6 months ago, created a question with more than 1,000 views. For To reassemble Illumina and PacBio, or just upgrade previous assembly with PacBio?
Popular Question 13 months ago, created a question with more than 1,000 views. For To reassemble Illumina and PacBio, or just upgrade previous assembly with PacBio?

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