User: CephBirk

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CephBirk0
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Posts by CephBirk

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Comment: C: Get bowtie2 to ignore isoform variants from Trinity assembly?
... Thanks! This is just what I was looking for and does shift about 20% of my reads from the "aligned concordantly >1 times" category to the "exactly one time" category. ...
written 4 days ago by CephBirk0
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Get bowtie2 to ignore isoform variants from Trinity assembly?
... So I've run bowtie2 against my Trinity assembly and get a high proportion of paired end reads that align concordantly at more than one place. I am suspicious that they're aligning to multiple isoform variants all from the same "gene" group. Fortunately, I've got a Trinity assembly that also include ...
rna-seq written 5 days ago by CephBirk0 • updated 5 days ago by h.mon25k
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Comment: C: RNASeq read coverage in protein space of MSA?
... I know I could just stick with the cDNA but the rest of the paper refers to various amino acid residues, so I thought it would be nice to show for example, that amino acid residue X has 400 read depth coverage supporting it. And for your second question, yes, I'm considering the consensus the majori ...
written 8 days ago by CephBirk0
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RNASeq read coverage in protein space of MSA?
... I used `samtools depth` to find the per base-pair read coverage over a number of isoform contigs from my Trinity assembly. I have also conducted a multiple sequence alignment of those isoforms using Clustal Omega. Now, in my final step, I want to assess the per-residue read coverage of the consensus ...
rna-seq written 10 days ago by CephBirk0
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Semicolon vs vertical line separating GO annotations in .go file
... I have a .go file from the supplementary material of a paper and am trying to understand the formatting. Here's a sample: Ocbimv22017828m GO:chromatin binding ; GO:0003682;GO:protein binding ; GO:0005515 Ocbimv22003392m GO:protein binding ; GO:0005515 Ocbimv22036412m GO:DNA binding ; GO ...
formatting gene ontology go written 9 months ago by CephBirk0 • updated 9 months ago by genomax68k

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