How is LINKS using .gv and .tsv files? about arcs HOT 6 CLOSED

The .gv file that ARCS outputs has to be converted in the .tsv file format LINKS understands.
For this, you must do the conversion using the makeTSVfile.py script. LINKS will then look for a file starting with a prefix (specified by the user, using -b. eg. -b links_c5r0.05e30000 In this case, LINKS will look for a file called links_c5r0.05e30000.tigpair_checkpoint.tsv).

The content of the file looks like:

500 r17141 f964157 1 10
500 r964157 f17141 1 10
500 f17141 r964257 7 70
500 f964257 r17141 7 70
500 f17141 f964300 1 10
500 r964300 r17141 1 10
500 f17141 r964336 1 10
500 f964336 r17141 1 10
500 r17141 f965243 1 10

Each row indicates a sequence pair.
The values are:

1. distance (arbitrarily set to 500 for ARCS). In a traditional LINKS k-mer based scaffolding, this is the distance between paired k-mers. This information is not used for ARCS scaffolding, but value must be there
2. first sequence ID. ID preceded with orientation f=plus strand, r=minus strand
3. second sequence ID. ID preceded with orientation f=plus strand, r=minus strand
4. number of supporting barcodes
5. estimates of the gap between the pair (arbitrarily set at 10 for ARCS, multiplicity of the 4th column. eg. 5 supporting barcodes, 50 must appear in this column)

I suggest you follow all the steps as outlined here:
ftp://ftp.bcgsc.ca/supplementary/ARCS/docs/arcsDemoScripts/readme.md

The most common source of error stems from draft genome sequence IDs. To avoid confusion, it is best to renumber your draft assembly, as suggested in the readme.

from arcs.

Okay, this makes sense. Following along with read me and the associated scripts there seems to be some differences between what the runmeTSV.sh is creating, specifically outputs that look like:

ws77111_c3r0.05e30000.tigpair_checkpoint.tsv

and then what the runLINKS.sh file is expecting (given your explanation), which is something like

links_c3r0.05e30000.tigpair_checkpoint.tsv

So then the output of runmeTSV.sh should just replace ws77111 with links?

from arcs.

the name of the file is controlled by the user (you), so yes, you have to ensure that whatever you name your BASENAME.tigpair_checkpoint.tsv file after the makeTSVfile.py step, you specify its BASENAME in LINKS using -b BASENAME

--Rene

from arcs.

Hi,
When I used the BASENAME, links didn't recognize the BASENAME.tigpair_checkpoint.tsv. Its log file always get:

Running: ../../../../software/links_v1.8.6/LINKS [v1.8.6]
-f ../Emu.Polished.Scaff10x_R2-renamed.fa
-s empty.fof
-m -d
-d 4000
-k 15
-e 0.5
-l 5
-a 0.3
-t 2
-o 0
-z 500
-b ../Emu.Polished.Scaff10x_R2-renamed.fa.scaff_s-empty.fof_d4000_k15_e0.5_l5_a0.3_z500_t2_o0_r-_p0.001_x0_m-d_pid47296
-r
-p 0.001
-x 0

The -b fellow is not the file I provided. Could you please help with this?
Thank you very much!

Best~
Jing

from arcs.

Yes, I get it. The -m is not needed.
Best~

from arcs.

@JhinAir - Yes, you don't need to include -m when using LINKS with ARCS. If you are unsure about what parameters you should specify, take a look at Examples/arcs-make - This is a Makefile that you can use to run the different steps of the ARCS pipeline (and optionally Tigmint).
You also need to take care to ensure that the -b basename specified matches the output of makeTSVfile.py (See @warrenlr 's comment above)

from arcs.