caaswxb / sry Goto Github PK

Hello Caa,

I am very please to use your script to identify and separate Y specific contigs from my male assembled genome,

i clone the script from the Github repository and ran, but i am getting the error message permission denied ,

Are there any specific requirements to make the script executable?. i install and exported it and all its dependencies to my path as indicated

/data/Project/illumina/SRY/M1$ /data/rnaah/software/SRY/SRY -m /data/Project/illumina/Male/Trimmomatic/trimmomatic1/trimmed_forward_paired.fq,/data/_Project/illumina/Male/Trimmomatic/trimmomatic1/trimmed_reverse_paired.f -f /data/Female/Trimmomatic/trimmomatic1/Female_Trimmed_ForwardF1_paired.fq,/data/Project/illumina/Female/Trimmomatic/trimmomatic1/Cylicomorpha_solmsii_Female_Trimmed_ReverseF1_paired.fq -l /data//HiFi_data_for_C_solmsii_male/raw_data/C01/Scaffolding/Trim_reads/Gapfilling2/test_racon.scaff_seqshh.fa -g 580 -p 20
-bash: /data/rnaah/software/SRY/SRY: Permission denied

Thanks for helping in anticipation,

Hello SRY team,

Thank you for creating an useful tool. I am currently trying to use it to assemble a better genome that includes sex chromosomes. I was curious about few things that I couldn't find in the readme/documentation. Could you share some insights please?

1. Could I use 100 samples (50 males and 50 females) when I run SRY program?
2. What is the relationship between the number of the samples, the size/quality of the genome and time taken to identify the Y chromosome reads?

Context:
I have a genome of a non-model organism with about ~450 contigs of which 21 are chromosome level scaffolds. This genome is from a male sample and is a heterogametic system (XY). Ideally. I would like to identify and stitch the sex chromosomes if possible. The genome was assembled using Hi-Fi and Hi-C data. I have Whole Genome Resequencing data from Illumina at ~30X coverage for about 50 males and 50 females .