Finding which contigs go into any given scaffold in an 454-Newbler assembly

Question

I guess there should be a quite simple script for calling which contigs go into which scaffolds. This is 454 data assembled with Newbler.

Thanks!

Answer 1

Thanks for the corrections ;)

A simple 'grep' on the 454Scaffolds.txt file gives me the folloving output.

-bash-3.2$ grep scaffold10511 454Scaffolds.txt scaffold10511 1 1251 1 W contig368342 1 1251 + scaffold10511 1252 2340 2 N 1089 fragment yes scaffold10511 2341 3244 3 W contig368343 1 904 + scaffold10511 3245 5704 4 N 2460 fragment yes scaffold10511 5705 6500 5 W contig368344 1 796 + scaffold10511 6501 7472 6 N 972 fragment yes scaffold10511 7473 10932 7 W contig368345 1 3460 + scaffold10511 10933 11579 8 N 647 fragment yes scaffold10511 11580 15817 9 W contig368346 1 4238 + scaffold10511 15818 19635 10 N 3818 fragment yes scaffold10511 19636 21767 11 W contig368347 1 2132 + scaffold10511 21768 22244 12 N 477 fragment yes scaffold10511 22245 25733 13 W contig368348 1 3489 + scaffold10511 25734 28642 14 N 2909 fragment yes scaffold10511 28643 32182 15 W contig368349 1 3540 +

As I understands it then this scaffold is based on contig368342-->368349, so that should answer this question ;)

Answer 2

Maybe you can also use grep -f :)