bedtools intersect mistakes

Question

[Oliver]

I am new to bioinformatics I have rna-seq data for analysis I did the folwing : I map the RNA-seq reads to the gene then I would like to use bedtools intersect my command is

bedtools intersect -a /mnt/s-ws/everyone/Drosera_rotundifolia.gff3 -b All_output.bam -wao

I got the error unable to open file "All_output.bam" my question should I create this file? and how?

[Carambakaracho]

I guess you need to elaborate a bit more - there's some inconsitencies in your question.

I map the RNA-seq reads to the gene

That usually would be a genome

I got the error unable to open file "All_output.bam"

Do you have a file All_output.bam? That should be the result of whatever alignement you did up in step one. What's the exact error message?

[ATpoint]

Use a dedicated RNA-seq tool such as featureCounts, htseq or quantify the fastq reads right away with something like salmon or kallisto against the reference transcriptome. Bedtools has many use-cases, RNA-seq is none of it.

By the way, if the message says not found means that the BAM file is missing. Do you have a BAM file?

[Oliver]

yes i found the file