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Old 06-13-2013, 05:59 AM   #1
flacchy
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Location: UK

Join Date: Apr 2013
Posts: 33
Default Velvet: how many reads into each contig

Hi,

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.

Last edited by flacchy; 06-14-2013 at 12:46 AM.
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