gen_raw_mask.pl not working correctly

[NicMAlexandre]

The faidx for my largest chromosome in the original assembly is as follows:

Chr1 196345723 6 60 61

The faidx for rawMask_35.fa and mask_35_50.fa show the following:

Chr1 5609878 6 60 61

I'm not sure why the size of my chromosome is so drastically reduced and I ave confirmed each previous step finished without error.

The following are my commands:

psmc/utils/./splitfa Sept22Assembly.fasta 35 | split -l 20000000 cat xaa xab xac > xxaa bwa index -a bwtsw genome.fasta bwa aln -R 1000000 -O 3 -E 3 genome.fasta xxaa > xxaa.sai bwa samse genome.fasta xxaa.sai xxaa > aln-se.sam samtools sort -n aln-se.sam -o aln-se_sorted.sam gzip aln-se_sorted.sam gzip -dc aln-se_sorted.sam.gz | perl seqbility-20091110/gen_raw_mask.pl > rawMask_35.fa seqbility-20091110/./gen_mask -l 35 -r 0.5 rawMask_35.fa > mask_35_50.fa

[NicMAlexandre]

We also tried the following with the same result:

psmc/utils/./splitfa genome.fasta 35 | split -l 20000000

#mappability_kmers.list contains the following xaa xab xac

for x in $(cat mappability_kmers.list); do bwa aln -R 1000000 -O 3 -E 3 -t 20 genome.fasta $x > ${x}.sai; done for x in $(cat mappability_kmers.list); do bwa samse genome.fasta ${x}.sai ${x} | samtools sort -o ${x}.bam; done samtools merge x.bam xaa.bam xab.bam xac.bam samtools sort -n x.bam -o x_sorted.bam samtools view -h x_sorted.bam | seqbility-20091110/gen_raw_mask.pl > raw_mask_35.fa seqbility-20091110/gen_mask -l 35 -r 0.5 raw_mask_35.fa > mask_35.fa

#head of mask_35.fa Chr1 5609912 15 60 61 Chr2 4270068 5703441 60 61 Chr3 3265589 10044692 60 61 Chr4 2067153 13364723 60 61 Chr5 1273941 15466344 60 61

[eroycroft]

Hi Nicolas - I know this is an old post, but wondering if you happened to work out the cause or fix for this issue? We're currently having the same problem. Cheers, Emily

[NicMAlexandre]

Hi Emily,

I was not able to sort out the issue. But I plan to use the software again soon and will hopefully find a solution.

On Mon, Oct 23, 2023 at 9:35 PM Emily Roycroft @.***> wrote:

Hi Nicolas - I know this is an old post, but wondering if you happened to work out the cause or fix for this issue? We're currently having the same problem. Cheers, Emily

— Reply to this email directly, view it on GitHub https://github.com/lh3/psmc/issues/38#issuecomment-1776525459, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFB6337MC5CP5ATCZLAUSJLYA5AQBAVCNFSM5FMINPTKU5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCNZXGY2TENJUGU4Q . You are receiving this because you authored the thread.Message ID: @.***>

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Nicolas Alexandre PhD Candidate, Integrative Biology Whiteman Lab University of California - Berkeley @.*** @.***>