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I ALSO WOULD LIKE To replace the small case c at the begining of chr by a capital case so my line is like this:


HWI-EAS422_12:4:1:69:89 GGTTTAAATATTGCACAAAAGGTATAGAGCGT U0 1 0 0 Chr8 6527777 F...

ok, i tried again with: less INPUT_FILE | perl -pe 's/ref_(chr\w+)\.fa/$1/' > OUTPUT_FILE and it works great!!!


I ALSO WOULD LIKE To replace the small case c at the begining of chr by a capital...

yes i would need this transformation to be applied to all the lines though, i will try it.

thanks for all your suggestion,
vgersh99 and ShawnMilo, I forgot to mention that the rest of the line is different for every line in my file.


cfajohnson, your suggestion is good, but i am...

I would like to remove characters from column 7 so that from an input file looking like this:


>HWI-EAS422_12:4:1:69:89 GGTTTAAATATTGCACAAAAGGTATAGAGCGT U0 1 0 0 ref_chr8.fa 6527777 F DD

I get...