User: Katie D

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Katie D0
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Posts by Katie D

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Comment: C: bedtools error: could not find indexes
... 2) I used Prodigal in the meta mode, because I am dealing with metatranscriptomes (bacterial community). I don't need to distinguish ncRNAs or 5' and 3' UTRs, I don't think. But, I thought I should define ORFs if I am interested in particular transcripts. Is this not so? Are you asking because there ...
written 13 months ago by Katie D0
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bedtools error: could not find indexes
... I want to use bedtools to count reads mapping back to genes, ultimately to use for differential expression analysis in edgeR. I used trinity to assemble my metatranscriptomes de novo, and bowtie2 to map raw reads back to the assembly. I seemingly sorted and indexed the file without a problem (return ...
bedtools rna-seq written 13 months ago by Katie D0 • updated 9 weeks ago by Biostar ♦♦ 20
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Comment: C: SortMeRNA starts, pauses, never finishes
... ./sortmerna --ref ./rRNA_databases/silva-bac-16s-id90.fasta,./index/silva-bac-16s-db:./rRNA_databases/silva-bac-23s-id98.fasta,./index/silva-bac-23s-db:./rRNA_databases/silva-arc-16s-id95.fasta,./index/silva-arc-16s-db:./rRNA_databases/silva-arc-23s-id98.fasta,./index/silva-arc-23s-db:./rRNA_databas ...
written 13 months ago by Katie D0
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SortMeRNA starts, pauses, never finishes
... Hi, I'm using SortMeRNA to remove rRNA reads from my RNA-seq data. I successfully used the program on multiple transcriptomes, but it just will not work for one of my files. It starts to run normally, and eventually pauses and never finishes. Eventually it just gets killed. Has anyone run into thi ...
sortmerna written 13 months ago by Katie D0
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Comment: C: Error Cutadapt: FASTQ file is expected to start with '@
... Hi! I am getting the same error as noe: cutadapt: error: Line 1 in FASTQ file is expected to start with '@', but found '\n' However, my file was always in fastq format and was not converted from sra or any other format, so I don't think that's the issue. head -n1 your.fastq this gives me @HS3:635 ...
written 13 months ago by Katie D0

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