User: madzayasodara

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Posts by madzayasodara

<prev • 12 results • page 1 of 2 • next >
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Comment: A: Obtaining Quality score of the mapped sequences - BBMap
... You guys sure there's not a sam/bamtools cmd that straight up does this? I did my alignment using BWA. I could loop through my 23 whole-genome bam files doing this, but It's gonna be real slow... ...
written 8 months ago by madzayasodara0
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Comment: C: Run a GO analysis for an non-model organism with annotation file
... Hummmm I'll check with my friend who annotated the genome, but I think they are orthologs. 1 - If they are, which tools you think I should use to run the enrichment analysis? 2 - If they aren't I was thinking of just running AmiGo (http://amigo1.geneontology.org/cgi-bin/amigo/term_enrichment), becau ...
written 13 months ago by madzayasodara0
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Comment: A: Run a GO analysis for an non-model organism with annotation file
... I have the HGNC symbol, so I am able to grab their GO term. Is it wrong to get the GO term from humans and use that for next steps? I'm just confused because the genes have been annotated already. So, it's not like I'm coming with only sequences with arbitrary IDs. ...
written 13 months ago by madzayasodara0
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Comment: C: Run a GO analysis for an non-model organism with annotation file
... Yes I have the sequences. But do I have to go from there? Why cant I use the GO terms for a close species based on my gene IDs? Thanks ...
written 13 months ago by madzayasodara0
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Run a GO analysis for an non-model organism with annotation file
... I have a list of genes of my non-model organism for which to run a GO analysis: RHOH UCHL1 ... I have a gtf file that looks like (not so much info there): scaffold_0 maker exon 9496 9623 . + . transcript_id "RHOH"; transcript_id_full "RHOH" s ...
genome next-gen written 13 months ago by madzayasodara0 • updated 4 months ago by rmash0
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Comment: C: Cufflinks gffread utility
... I cleaned the .gtf from some genes (4 of them) and it run without warnings, but I'm not clear this is how I should have proceeded. ...
written 14 months ago by madzayasodara0
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Comment: A: Cufflinks gffread utility
... Hello! Any ideas why I'm getting a seg fault when I run this? gffread BF_annotation.gtf -W -O -E -L -F -w BF_transcripts.fa -g BF_genome.fa GFF Warning: merging overlapping/adjacent feature segment exon (8436614-8437382) with exon (8436535-8436613) for GFF ID KDM4A on scaffold_1 GFF War ...
written 14 months ago by madzayasodara0
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Get sequences for all genes in a GTF file
... I have a gtf file like: scaffold_0 maker exon 9496 9623 . + . transcript_id "RHOH"; transcript_id_full "RHOH" scaffold_0 StringTie exon 11728 11971 . + . transcript_id "RHOH"; transcript_id_full "RHOH" scaffold_0 ...
genome assembly written 14 months ago by madzayasodara0
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Comment: A: how to use Lastz "multiple contains"?
... Hey! Did you figure this out? I have the same issue. ...
written 19 months ago by madzayasodara0
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Cross-species coordinate conversion
... Hi! I have a still unpublished genome assembly, which I used to map and annotate my DNA-Seq pop data. I want to use the ref the zebra finch genome available from ensembl as my ancestral ref in some pop gen analysis. For this, I would have to have the zebra finch genome have the same coordinates as ...
assembly written 19 months ago by madzayasodara0

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