[Lszar]

That would definately take ages when you are dealing with millions of reads..Best thing would be using AMOS package.

convert the afg file output by velvet to a bnk file

~/src/amos-3.0.0/src/Bank/bank-transact -m my.afg -b my.bnk -c

run depth-of-coverage output

~/src/amos-3.0.0/src/Validation/analyze-read-depth my.bnk -d -r > Outputfile

The output file contains the contigs ID, Corresponding reads, depth of contig. etc..Hope this helps someone

Hi Icebreaker,

I'm trying to do exactly what suggested, but I'm unsuccessful. After both commands the result was a directory/, and the output file have this appearance:

1 23 74 74 38.5676 38.5676
2 71 54 54 170.148 170.148
3 49 50 50 136.52 136.52
4 89 54 54 223.463 223.463
5 45 64 64 98.9375 98.9375
6 3 141 141 3.21277 3.21277
7 1 108 108 1.39815 1.39815
8 20 64 64 42.6719 42.6719
9 62 54 54 158.611 158.611
10 10 64 64 22.4375 22.4375
11 37 61 61 77.1639 77.1639
12 32 242 242 17.0579 17.0579
13 20 57 57 51.0175 51.0175

I can't understant this file and I don't see contigs ID, Corresponding reads, depth of contig. etc, as you explained.
Can you help me?
Thanks
Lszar

[Lszar]

Hi, I guess this is the right place to ask...

I am trying to figure out how many reads made it into each contig after I run velvet. I used the flag -read_trkg yes and -amos_file yes.
I found some advise online on how to process them but I am a bit stuck.
So from the amos file I have tried this path:

$ /home/admin/amos-3.1.0/src/Bank/bank-transact -m velvet_asm.afg -b velvet_asm.bnk -c

and then
$/home/admin/amos-3.1.0/src/Validation/analyze-read-depth velvet_asm.bnk -i -d -r > output

The problem is that the file output is something like this :
1 1646 1340 1340 108.275 108.275
2 1 97 97 1.03093 1.03093
3 2085 1589 1589 113.904 113.904
4 175 75 75 219.547 219.547
5 187 162 162 105.944 105.944
6 124 76 76 157.171 157.171
7 1023 768 768 112.914 112.914
8 9 99 99 9.09091 9.09091
9 151 168 168 72.8214 72.8214
10 2224 1602 1602 123.306 123.306
11 6582 5312 5312 107.116 107.116
12 2850 2487 2487 98.653 98.653
13 3 105 105 2.62857 2.62857
14 3 103 103 2.91262 2.91262
15 4350 3350 3350 115.28 115.28
16 1788 1268 1268 128.341 128.341
17 1746 1325 1325 116.024 116.024

could anyone tell me what the filed are or if there is a different way to get the information I need??

Thank you,

F.

Hi Flacchy, do you solve your questions?
I'm having the same problem now, that you have time, time ago.
If you have some solution, please, let me know.
Thanks
Lszar