User: jstevenson2256

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Posts by jstevenson2256

<prev • 9 results • page 1 of 1 • next >
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How do I find the same gene in two different assemblies?
... I have two genome assemblies from two phenotypes of a non-model ant species. I have performed gene prediction on them both and have found a difference in the number of predicted genes. How do I find these differing genes? I can't compare gene IDs as they will be different in both assemblies and I ca ...
genome assembly alignment rna-seq written 3 days ago by jstevenson225610
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Gene Enrichment of a Non-Model Organism - Advice Please?
... **What I've done so far:** I've got RNAseq data from a non-model insect (ant) species and have aligned them to a genome assembly in STAR. This was fed into BRAKER2 (wrapper of GeneMark-ET and AUGUSTUS) to predict genes. With lists of nucleotide and amino acid sequences output from BRAKER of each pre ...
gene assembly rna-seq enrichment written 8 days ago by jstevenson225610
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Comment: C: SCRMshaw Enrich: Undefined symbol: Perl_xs_boot_epilog
... Ah, sorry, I shortened the path in the question for ease of reading, I've updated it to avoid confusion, Anaconda isn't in the root directory. ...
written 13 days ago by jstevenson225610
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SCRMshaw Enrich: Undefined symbol: Perl_xs_boot_epilog
... I'm using SCRMshaw to predict CRMs and I'm trying to use the enrichment bash script that comes with it. At first it had the problem of `Can't locate Bio/SeqIO.pm in @INC` but this was fixed by exporting the path to a BioPerl installation in an Anaconda environment I made for SCRMshaw (`export PERL5L ...
perl scrmshaw software error crms written 13 days ago by jstevenson225610
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Answer: A: Problem with PASA Pipeline Installation Configuration
... Issue fixed, see https://github.com/PASApipeline/PASApipeline/issues/104 ...
written 24 days ago by jstevenson225610
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Problem with PASA Pipeline Installation Configuration
... I've installed PASA and am trying to configure it for alignment assembly using the sample data supplied. I try running the pipeline using the commands given on the wiki (https://github.com/PASApipeline/PASApipeline/wiki/PASA_alignment_assembly): $PASAHOME/Launch_PASA_pipeline.pl \ -c ...
software error assembly pasa alignment written 24 days ago by jstevenson225610
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Comment: C: Samtools segmentation fault when extracting exons from bam file.
... Thank you! It worked wonderfully. ...
written 6 weeks ago by jstevenson225610
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Comment: C: Samtools segmentation fault when extracting exons from bam file.
... Excellent, thank you! Converting to a .bed file and using the -L command worked fabulously. Final script looks like: samtools view -@ 8 -b -h -L exons.bed alignment.bam > exon_alignments.bam ...
written 6 weeks ago by jstevenson225610
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Samtools segmentation fault when extracting exons from bam file.
... I have a bam file of RNAseq alignments generated by STAR (alignment.bam) and a list of possible exon positions in a txt file (exons.txt). I'm trying to extract these exons from the alignment file and to do so I'm using a samtools view loop: #!/usr/bin/env for line in `cat exons.txt`; do ...
alignment samtools rna-seq seg fault written 7 weeks ago by jstevenson225610 • updated 7 weeks ago by Damian Kao15k

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Scholar 24 days ago, created an answer that has been accepted. For A: Problem with PASA Pipeline Installation Configuration

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