Tag: smallRNAseq

I cannot obtain summary alignment with Bowtie2

I cannot obtain summary alignment with Bowtie2 1 Hello everyone, I am aligning my Small RNA Seq data with Bowtie 2. Although the alignment performs well, the only information I obtain after finishing running the alignment is the following: ## Time loading reference: 00:00:00 ## Time loading forward index: 00:00:00…

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Kraken2 + Bracken with short reads (~20 bases) as input

Kraken2 + Bracken with short reads (~20 bases) as input 0 I have small RNA sequencing data (fastQC read length graph below) from rat tissue across two conditions and would like to investigate the presence of microbiome-sourced RNA. I have added the read length graph from an example fastQC report….

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smallRNA profiling using HTSeq error

smallRNA profiling using HTSeq error 1 Hello, I want to create a “count” file using HTseq. I have both BAM file and gtf file: htseq-count -f bam -s no -i AK1a_clean_Aligned.sortedByCoord.out.bam gencode.v42.chr_patch_hapl_scaff.annotation.gtf >> AK1a_counts.txt It still gives an error: htseq-count: error: the following arguments are required: featuresfilename Can someone please…

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how to use old and new smallRNAseq data sets for data analysis

how to use old and new smallRNAseq data sets for data analysis 0 I have some smallRNAseq data (already sequenced) and would like to generate smallRNAseq from another few samples. but at the end I would like to include both new and old batches in the data analysis. For smallRNA…

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