hello every one,
as i am working on count based differential analysis and for that i am trying to use HTSEQ and bedtools
1. I am using Bedtool to count read in as
here in spite of bed file i am using reference genome file all.gff3. is it correct to use it ?
Because I am not sure that I will get proper result with these gff3 file or not
2. I am getting error with ht-seq as it is already installed in my machine but still it is showing that
Kindly reply me
Thanks
as i am working on count based differential analysis and for that i am trying to use HTSEQ and bedtools
1. I am using Bedtool to count read in as
Code:
bedtools multicov -bams sample1.bam sample2.bam sample3.bam -bed all.gff3
Because I am not sure that I will get proper result with these gff3 file or not
2. I am getting error with ht-seq as it is already installed in my machine but still it is showing that
Code:
[root@localhost ~]# htseq-count bash: htseq-count: command not found...
Thanks
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