LASeR, no simulated reads

[azure-twilight]

I use VISOR v1.1 to simulate long reads. There is no error reported in LASeR step but it does not simulate reads, as the final bam file has no information in it. What's wrong with this?

[davidebolo1993]

Hi @azure-twilight,

sorry for being late. That's indeed strange. I'm using LASeR quite frequently and this is never happening. Can you elucidate a bit more on your case ? (command line used and stuff like that...).

Thanks,

Davide

[azure-twilight]

I use this command for a test: VISOR LASeR -s ins -g ref.fasta -o ins0 --coverage 2 -b LASeR.bed --threads 4 And it runs without errors, but when simulating, it produces .fq files with size 0.

Lucky I found an old version of VISOR in my evironment and it runs correctly, but I still don't know what happens with the newest version of VISOR.

[davidebolo1993]

Hi @azure-twilight,

can you share your reference FASTA, hack and laser BED? I definitely need to try to replicate the issue to check if there's something wrong with LASeR. Thanks,

Davide

[davidebolo1993]

Any updates on this?

[davidebolo1993]

Closing for the time being. Feel free to re-open at anytime.

[cytham]

@davidebolo1993 I am having the same issue. Got a bam file containing only the header.

My command VISOR LASeR -g ../resource/human_hs37d5.fasta -s chm1/ -b ../resource/SV_evaluation/SHORtS.LASeR.bed -o 10x_20k_90 --coverage 10 --identity_min 90 --length_mean 20000 --read_type pacbio --threads 40

Do you have an email for me to send you the fasta, hack and laser beds?

[davidebolo1993]

Hi @cytham,

Sure, reach me out @ davidebolognini7@gmail.com. Thanks,

Davide

[davidebolo1993]

Just for future reference, this was caused by 0s being used in SHORtS.LASeR.bed instead of 1s (start coordinates) when simulating chromosome-long regions (VISOR LASeR).

[LYC-vio]

Hi @davidebolo1993, I met the same issue here, and changing from 0s to 1s didn't help

the HACK and LASeR commands I used were:

ref=hs37d5.fa
bed=sim_dup.bed
hapdir=simulated_genome_dup

bed_LASeR=LASeR.bed
cov=40
outdir_LASeR=Reads_dup_${cov}x

VISOR HACk -g ${ref} -b ${bed} -o ${hapdir}
VISOR LASeR -g ${ref} -s ${hapdir} -b ${bed_LASeR} -o ${outdir_LASeR} --coverage ${cov} --threads 16 --fastq --compress

The VISOR I used was the v1.1.2 on anaconda reference was downloaded from: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz sim_dup.bed and LASeR.bed were from here: https://github.com/tjiangHIT/cuteSV/tree/master/simulation I manually changed 0s in column 2 of LASeR.bed to 1s, but the output fq file was still empty.

Could you give me some help on this?

Best