User: rgn5011

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rgn50110
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Posts by rgn5011

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Answer: A: Using gffread to extract annotated fasta sequences from a genome
... Feel free to post a fix to this, but I did eventually find an old version that can be installed with conda (`conda install -c bioconda gffread=0.9.8-0`) which gives Gene id, gene name, and CDS is the fasta output file ...
written 28 days ago by rgn50110
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Using gffread to extract annotated fasta sequences from a genome
... I am trying to extract annotated fasta sequences from a genome file, using a gff file and `gffread` (version 0.9.8-0). The code that I found is simply `gffread -w test.transcripts.fa -g genome.fna test.gff`and this works great on my local mac. Some example output can be seen below: > gene-TM ...
genome gff alignment sequencing written 28 days ago by rgn50110
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Answer: A: Analyzing only forward reads in mothur
... Hey guys, I know this is over a year old but I found out something that can fix this. Currently we are using mothur to analyze our PacBio data which comes as a bam file. We then convert the bam to a fastq file and ran into the same issue mentioned above. So lets say I have 5 samples after we conve ...
written 2.1 years ago by rgn50110

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Scholar 28 days ago, created an answer that has been accepted. For A: Using gffread to extract annotated fasta sequences from a genome

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