Scaffolding with linked reads

[Nayeli Gutiérrez]

Hi everyone,

I ran abyss twice on the same genome, one without any extra dataset for scaffolding and the second using linked reads. Both had exactly the same stats values. Is this normal? Shouldn't I expect some minimal differences? I just want to make sure abyss DID use the linked reads for guiding scaffolding.

This is the script I used:

abyss-pe k=27 name=Tdiscoideus2 lr='tet' tet='/home/ngutierrez/nas4/linked_reads_output/barcoded.fastq.gz' in='/home/ngutierrez/nas4/abyss/trimgalore_output/Tdiscoideus2_R1_001.trimmed.fastq.gz /home/ngutierrez/nas4/abyss/trimgalore_output/Tdiscoideus2_R2_001.trimmed.fastq.gz'

Barcodes of linked reads were treated using the longranger basic command as indicated in the abyss manual.

Any help would be appreciated,

Nayeli

[Lauren Coombe]

Hi Nayeli,

Can you confirm whether the Tigmint and ARCS steps ran, based on the log files? You could also look for files named (for example) Tdiscoideus2-8.tigmint.arcs.fa in your working directory to determine whether those steps were executed.

Thanks!

Lauren

[Nayeli Gutiérrez]

Hi Lauren,

Thanks for your reply!

I checked and no files with the sufix tigmint.arcs.fa or similar were generated although I made sure Tigmint and ARCS are installed and running and the linked reads are in the path I indicated. Do you think it has something to do with the script?

The log files and scripts of both runs are attached in case they are useful.

Best,
Nayeli

[Lauren Coombe]

Hi Nayel,

From your script, it appears that you are using quite an old version of ABySS (2.0.2)? The added support for running Tigmint and ARCS was added in version 2.1.0, so you need to use that version or later to take advantage of that functionality.

Best,

Lauren