Question: bedtools intersect mistakes
0
gravatar for Oliver
6 months ago by
Oliver0
Oliver0 wrote:

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?

rna-seq • 229 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by Oliver0

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?

ADD REPLYlink written 6 months ago by Carambakaracho2.0k

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?

ADD REPLYlink modified 6 months ago • written 6 months ago by ATpoint31k

yes i found the file

ADD REPLYlink written 6 months ago by Oliver0
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