Tag: RCorrector

Interpreting Hisat2 alignment output

Interpreting Hisat2 alignment output 1 I am am aligning my RNAseq data to a reference genome using Hisat2 for the first time and I have what I am sure is a basic question. However I am still confused after reading a number of online resources. Broadly, my pipeline goes from…

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“bowtie2 died with signal 9 (KILL)” error message, having trouble figuring out how to fix my script

Hello! I am working on assembling a transcriptome of the terminal ganglion of the cricket (Gryllus bimaculatus). We are working on a non-model species and thus did not remove ribosomal contamination during library prep. We want to remove ribosomal contamination bioinformatically, and I am mapping our sequences, which have been…

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Is it normal for RCorrector to remove millions of reads?

Is it normal for RCorrector to remove millions of reads? 0 I’m trying to build De Novo transcriptomes for unsequenced plants to do sequence analysis. I’m trying to choose a tool for my first pass of quality filtering after running FastQC on my raw reads. I’ve tried AfterQC and RCorrector….

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