bedtools, linux, rnaseq

Question

[Daniel James]

I have 6 files where I have the number of reads mapping to each gene on chr22. and a a Rnagene file which has number of reads mapping every gene. How do I create a tab delineated file contianing the number of reads mapping to each gene on chr22 using coverage bed ?

Answer 1

[Devon Ryan]

join, a little python script, a little perl script, R, grep, etc.

There are many ways to do this. What have you tried that didn't work?

[Daniel James]

i did it using join but I am unable to add a header to the table

[Alex Reynolds]

The join tool glues columns. You could use a different tool to write a header, such as awk, echo, Perl, Python, etc. What else have you tried?

Answer 2

[Alex Reynolds]

If you want to write a header, you could use a variety of tools, such as awk, echo and others.

For example, to add the tab-delimited header A \t B \t C to foo.txt:

$ awk 'BEGIN{print "A\tB\tC"} {print $0;}' foo.txt > foo-with-header.txt

Or via echo:

$ echo -e "A\tB\tC" | cat - foo.txt > foo-with-header.txt

Lots of ways to do this.