User: kallen83

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kallen8310
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Posts by kallen83

<prev • 6 results • page 1 of 1 • next >
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Comment: C: finding contigs present in one assembly but missing from another
... thanks, I'll have a look at that ...
written 5 months ago by kallen8310
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Comment: C: finding contigs present in one assembly but missing from another
... the complicating feature of that approach is repetitive elements missed by DUST and the relevant repetitive elements databases. At a first look it appears I'll need to build a repetitive element db for this species before I can proceed with something like that. ...
written 5 months ago by kallen8310
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finding contigs present in one assembly but missing from another
... I have two pacbio assemblies for the same plant species, and I need to determine if there are regions represented in one assembly that are missing from the other. I have tried using progressiveMauve, and while I suspect that the information I'm looking for is somewhere in the output I'm having a ha ...
genome assembly alignment written 5 months ago by kallen8310
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Comment: C: Tophat 2.1.1 failing to recognize fasta file
... the blank line between the two fasta records is an artifact of cutting and pasting from a terminal window. It's not present in the actual fasta file. But your second point is very interesting, I didn't know the field moved on, I'm going to read that paper right now (and I have -cough- ways -cough- ...
written 14 months ago by kallen8310
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Comment: C: Tophat 2.1.1 failing to recognize fasta file
... Yeah, I tried that, with the id lines changed just the way you suggested, but I get the same result. ...
written 14 months ago by kallen8310
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Tophat 2.1.1 failing to recognize fasta file
... I'm trying to align a set of reads in fasta format to a reference genome (indexed with bowtie2-build), but tophat is failing with the following error: tophat thc_genomic 5369.fa [2017-04-20 10:14:53] Beginning TopHat run (v2.1.1) ----------------------------------------------- ...
alignment rna-seq written 14 months ago by kallen8310 • updated 14 months ago by genomax49k

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