twoBitToFa usage

[prasai]

Hi, I am having problem with using twoBitToFa -seqList=file command

I tried with start=X, end=X. and these are working properly but I used my command as

twoBitToFa -seqList=chr1:28735-29810 hg19.2bit hg.fa
Couldn't open chr1:28735-29810 , No such file or directory

and also tried
twoBitToFa -seqList=chr1 hg19.2bit hg.fa
Couldn't open chr1 , No such file or directory

can any one please hel me to sort this problem?
Thanks in advance

[winsettz]

-seqList=file

looks for a file that has those parameters, you don't put them there directly.

[m@k4 hg19]$ ./twoBitToFa hg19.2bit:chr1:28735-29810 test.fa
[m@k4 hg19]$ head test.fa
>chr1:28735-29810
CGCCTCTTTGGGACCGCGGTTTATACTTTCGAAGTGCTCGGAGCCCTTCC
TCCAGACCGTTCTCCCACACCCCGCTCCAGGGTCTCTCCCGGAGTTACAA
GCCTCGCTGTAGGCCCCGGGAACCCAACGCGGTGTCAGAGAAGTGGGGTC
CCCTACGAGGGACCAGGAGCTCCGGGCGGGCAGCAGCTGCGGAAGAGCCG
CGCGAGGCTTCCCAGAACCCGGCAGGGGCGGGAAGACGCAGGAGTGGGGA
GGCGGAACCGGGACCCCGCAGAGCCCGGGTCCCTGCGCCCCACAAGCCTT
GGCTTCCCTGCTAGGGCCGGGCAAGGCCGGGTGCAGGGCGCGGCTCCAGG
GAGGAAGCTCCGGGGCGAGCCCAAGACGCCTCCCGGGCGGTCGGGGCCCA
GCGGCGGCGTTCGCAGTGGAGCCGGGCACCGGGCAGCGGCCGCGGAACAC

Hope that helps!

[prasai]

Thank you, It really helped me