bedtools intersect mistakes
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?
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I guess you need to elaborate a bit more - there's some inconsitencies in your question.
That usually would be a genome
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?Use a dedicated RNA-seq tool such as
featureCounts,htseqor quantify the fastq reads right away with something likesalmonorkallistoagainst the reference transcriptome. Bedtools has many use-cases, RNA-seq is none of it.By the way, if the message says
not foundmeans that the BAM file is missing. Do you have a BAM file?yes i found the file