Comments (6)
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:
- 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
- first sequence ID. ID preceded with orientation f=plus strand, r=minus strand
- second sequence ID. ID preceded with orientation f=plus strand, r=minus strand
- number of supporting barcodes
- 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.
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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)
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Related Issues (20)
- About Running ARCS in default mode HOT 3
- GCC version update HOT 1
- arcs-1.2.2: abyss-fixmate-ssq sometimes segfaults HOT 9
- Short read length question: can the tool accept 250? HOT 2
- arcs-long: tiny PE-pairs are produced HOT 3
- Scaffolding Expectations HOT 12
- Running ARCS and ARKS HOT 2
- Parameters for corrected ONT reads HOT 2
- arcs-make in bin HOT 2
- Add optional dependency of pigz HOT 1
- unrecognized option '--fastq' HOT 3
- fastq formatting barcodes in BX tag HOT 8
- ARKS fails to create any links with a highly repetitive input HOT 4
- Parameters for PacBio HiFi data HOT 3
- Can this software use HiC data, or need to use the sequencing technology mentioned in your paper? HOT 1
- `arcs-tigmint` and `arks-tigmint` struggle with input files outside working directory HOT 3
- Incorrect program call? HOT 6
- `arcs-long`/`arks-long` vs `LINKS`? HOT 2
- Understanding specific scaffolding output HOT 4
- tigmint-make 'missing separator' error HOT 8
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