User: James Sacco

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Posts by James Sacco

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Comment: C: HTSeq Import Error Re: Working vs Build Directory
... The solution was that I had remove htseq from both my conda environment and system (in site-packages), and then install a version of htseq that was compatible with python2. I found that at https://anaconda.org/bcbio/htseq ...
written 8 days ago by James Sacco0
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Comment: C: SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation in
... Thank you @GenoMax! This helps tremendously! The seqkit command worked perfectly! ...
written 15 days ago by James Sacco0
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Comment: C: SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation in
... I found out my reads were the reverse complement of what I needed to run my analysis (in a program downstream of this step). I did send the output to a new file (with >), which messed up the fastq format, but did have the reverse complements. ...
written 18 days ago by James Sacco0
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Comment: C: SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation in
... Reposting because I accidentally posted as a reply: I am trying to transform some fastq.gz files to their reverse complement, but when I run the command seqkit seq hairpin.fastq.gz -r -p I get the output printing to the console. Is that what this function is supposed to do? I want to edit the ...
written 18 days ago by James Sacco0
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Comment: C: SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation in
... Hello, I am trying to transform some fastq.gz files to their reverse complement, but when I run the command seqkit seq hairpin.fastq.gz -r -p I get the output printing to the console. Is that what this function is supposed to do? I want to edit the file itself. Thank you ...
written 18 days ago by James Sacco0
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Comment: A: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scri
... Thank you for sharing this. I find it essential training, especially working with such large data. Always good to keep sharp. ...
written 19 days ago by James Sacco0
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Comment: C: HTSeq Import Error Re: Working vs Build Directory
... I am running it from the directory seen above in the ImportError, except at `~/Bioinformatics/softwares/guideseq/` It is the same directory with the setup.py and requirements.txt ...
written 20 days ago by James Sacco0
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HTSeq Import Error Re: Working vs Build Directory
... **Problem:** I am trying to run a python3 script that imports HTSeq, but I have a conflict regarding the "build directory." **Background:** I have set up a python3 conda environment on my Ubuntu virtual machine. I git cloned the python2 package, and pip installed the requirements.txt, yet when I g ...
htseq software error next-gen rna-seq written 20 days ago by James Sacco0

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Autobiographer 20 days ago, has more than 80 characters in the information field of the user's profile.
Supporter 3.7 years ago, voted at least 25 times.

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