Name | Modified | Size | Downloads / Week |
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Parent folder | |||
dsimM252v1.2.gtf.gz | 2023-05-05 | 4.4 MB | |
prepare_annotation.Rmd | 2023-05-05 | 31.1 kB | |
dsimM252v1.2.fa.README | 2023-05-05 | 1.2 kB | |
Totals: 3 Items | 4.4 MB | 0 |
bcftools consensus -f dsimM252v1.1.fa -i 'QUAL>0 & REF~"N" & (GT="1/1" | GT="2/2") & STRLEN(ALT)=STRLEN(REF)' Pool_25a_nlocs.vcf.gz > dsimM252v1.2.fa # number of Ns remaining [vetlinux05@pgnsrv043 M252_Nlocs]$ sed '/^>/d;s/[^N]//g;/^$/d' dsimM252v1.2.fa | tr '\n' '+' | sed 's/+//g' | wc -c 838158 [vetlinux05@pgnsrv043 M252_Nlocs]$ sed '/^>/d;s/[^N]//g;/^$/d' dsimM252v1.1.fa | tr '\n' '+' | sed 's/+//g' | wc -c 856534 # only named chromosomes incl. mtDNA [vetlinux05@pgnsrv043 M252_Nlocs]$ sed '/^>/d;s/[^N]//g;/^$/d' 1.fa | tr '\n' '+' | sed 's/+//g' | wc -c 513866 [vetlinux05@pgnsrv043 M252_Nlocs]$ sed '/^>/d;s/[^N]//g;/^$/d' 2.fa | tr '\n' '+' | sed 's/+//g' | wc -c 502052 # only 2L, 2R, 3L, 3R, 4, X [vetlinux05@pgnsrv043 M252_Nlocs]$ sed '/^>/d;s/[^N]//g;/^$/d' 1.fa | tr '\n' '+' | sed 's/+//g' | wc -c 363190 [vetlinux05@pgnsrv043 M252_Nlocs]$ sed '/^>/d;s/[^N]//g;/^$/d' 1.fa | tr '\n' '+' | sed 's/+//g' | less -S [vetlinux05@pgnsrv043 M252_Nlocs]$ sed '/^>/d;s/[^N]//g;/^$/d' 2.fa | tr '\n' '+' | sed 's/+//g' | wc -c 353967 # fills in close to 18000 Ns without changing the sequence lengths, about half of them in the major chromosomes