gene_x 0 like s 410 view s
Tags: database
TODO: after annotation check if the app-gene has been truncated in 5179-R1. The 5179 generates 180 kDa and 220 kDa (isoforms) while 5179-R1 generated only a 140 kDa protein.
# See the paper: Induction of Staphylococcus epidermidis biofilm formation via proteolytic processing of the accumulation-associated protein by staphylococcal and host proteases
#------------ 5179 ------------
# -- from unicycler (5179_bold) --
total 16 4 2,524,342 2,469,173 2,469,173
1 1 1 2,469,173 2,469,173 2,469,173 complete
2 1 1 17,749 17,749 17,749 complete
3 1 0 4,761 4,761 4,761 incomplete
4 1 1 4,595 4,595 4,595 complete -->
5 1 0 3,735 3,735 3,735 incomplete
6 1 0 3,718 3,718 3,718 incomplete
7 1 0 3,573 3,573 3,573 incomplete
8 1 1 2,449 2,449 2,449 complete -->
9 1 0 2,411 2,411 2,411 incomplete
10 1 0 2,371 2,371 2,371 incomplete
11 1 0 2,365 2,365 2,365 incomplete
12 1 0 1,637 1,637 1,637 incomplete
13 1 0 1,568 1,568 1,568 incomplete
14 1 0 1,505 1,505 1,505 incomplete
15 1 0 1,403 1,403 1,403 incomplete
16 1 0 1,329 1,329 1,329 incomplete
1 2,469,173 1.00x UniRef90_Q5HJZ9 1,901,872 reverse 100.0% 100.0%
2 17,749 2.27x UniRef90_A0A0H2VIR3 4,771 forward 93.2% 99.7%
4 4,595 10.19x none found (Submitted!)
8 2,449 17.14x none found (Submitted!)
# -- from trycycler (Submitted after adding the contig 4 and 8 since longer!) --
cluster_001_consensus 2471445 23 70 71 (Submitted!)
cluster_002_consensus 17749 23 70 71 (Submitted!)
#------------ 5179-R1 ------------
# -- from unicycler (5179R1_normal) --
Component Segments Links Length N50 Longest segment Status
total 2 2 2,486,311 2,468,563 2,468,563
1 1 1 2,468,563 2,468,563 2,468,563 complete
2 1 1 17,748 17,748 17,748 complete
# -- from trycycler --
cluster_001_consensus 2470004 23 70 71 (Submitted!)
cluster_002_consensus 17748 23 70 71 (Submitted!)
luster_003 with only one contig
luster_004 with only one contig
luster_005 with only one contig
#makeblastdb -in 5179_trycycler_chr.fasta -dbtype nucl
#blastn -db 5179_trycycler_chr.fasta -query 2-16.fasta -out 2-16_vs_trycycler_1.blastn -evalue 0.00000000001 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1
#------------ 1585 ------------
# 1585_normal/unicycler/chrom_plasmids.fasta
# -- from unicycler (1585_normal) --
Segment Length Depth Starting gene Position Strand Identity Coverage
1 2,443,574 1.00x UniRef90_Q5HJZ9 1,085,369 forward 99.3% 100.0%
2 9,014 3.72x none found
7 2,344 11.44x none found
8 2,255 9.81x none found
# after correction using polypolish and polca (see ~/DATA/Data_Holger_S.epidermidis_1585_5179_HD05/1585_normal/unicycler)
1 2443600 3 70 71 (Submitted!)
2 9014 2478515 70 71 (Submitted!)
7 2344 2487661 70 71 (Submitted!)
8 2255 2490042 70 71 (Submitted!)
# -- from trycycler --
cluster_001_consensus 2443176 23 70 71
cluster_002_consensus 9014 23 70 71
cluster_003_consensus 2255 23 70 71
cluster_004_consensus 2344 23 70 71
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