User: Shred

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Shred220
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Posts by Shred

<prev • 59 results • page 1 of 6 • next >
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Comment: C: How to get the output on multiple files into one file in sbatch script?
... Why not using a `for` loop to call each bam file? You could get the filename into a variable and you could echo first the `filename` than the `output` ...
written 4 days ago by Shred220
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Comment: C: Difference in the counts generated using FeatureCounts and HTseq
... Why you've used the "Tool" tag for a question? You must include the syntax used for htseq-count and featurecounts. ...
written 4 days ago by Shred220
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Comment: C: How to remove fasta headers in a multifasta file and write file name as a fasta
... He said he's already got the concatenated file. ...
written 7 days ago by Shred220
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Answer: A: How to remove fasta headers in a multifasta file and write file name as a fasta
... Assuming you're using BASH, use `basename` to get the filename with no PATH. Like: filename=$(basename -i file | cut -d'.' -f1) Then you could replace it using sed sed -i "s/^\>.*$/$filename/" your.fasta Remember to use double quotes to use variables in sed. ...
written 7 days ago by Shred220
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Comment: C: Extend 3' UTR of a GTF file
... Hi, as explained, there's a need for a data driven approach (I'm working on..). Here the problem is with a 3' RNA-seq, which produces reads in a different way than a standard TruSeq: tools for annotations rely on reads across whole genes, so they're not designed to work with this sequencing strategy ...
written 18 days ago by Shred220
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Tool: Extend 3' UTR of a GTF file
... Hello guys. Some times ago I've asked here if there's an existing approach designed to extend 3' terminus of genes by a provided length: I received no answers, because apparently there's no one. In my team we encountered this needing because of a 3' RNA-seq project against a poor annotated genome: ...
gtf annotation tool rna-seq python written 20 days ago by Shred220
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Comment: C: How to retrieve sequences of genes list at a time from a fasta file
... Convert the CRFL line terminators with Unix one (LF). The simplest way is with [dos2unix][1] or with a text editor (not suggested for huge text file). [1]: http://(http://manpages.ubuntu.com/manpages/trusty/man1/dos2unix.1.html) ...
written 24 days ago by Shred220
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Comment: C: Tips for Reading genotype files into python
... Please do not cross post into more forum at the same time. This is considered a bad practice. ...
written 24 days ago by Shred220
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Comment: C: Tips for Reading genotype files into python
... What's the input format? TSV? Are you expecting an output with SNPs as header and observations (?) as rows? If so, maybe would be better to load into a Dataframe with Pandas' module [read_csv][1] [1]: https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.read_csv.html ...
written 24 days ago by Shred220
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Comment: C: Tips for Reading genotype files into python
... Please post input details and desired output and the code you've used too. ...
written 25 days ago by Shred220

Latest awards to Shred

Scholar 7 days ago, created an answer that has been accepted. For A: GenBank features don't extract sequences based on condition Biopython
Great Question 18 months ago, created a question with more than 5,000 views. For Faster way to get GC content and Coverage from .fasta
Popular Question 18 months ago, created a question with more than 1,000 views. For Avoid download limit from NCBI entrez with Biopython using API key
Popular Question 18 months ago, created a question with more than 1,000 views. For Trim sequences based on alignment in python
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: How can I find the same record in two file? Use python
Scholar 21 months ago, created an answer that has been accepted. For A: Faster way to get GC content and Coverage from .fasta
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Faster way to get GC content and Coverage from .fasta
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: How can I find the same record in two file? Use python
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: How can I find the same record in two file? Use python
Scholar 2.6 years ago, created an answer that has been accepted. For A: Faster way to get GC content and Coverage from .fasta

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