Xanthomonas oryzae: Difference between revisions
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Location: /fs/szasmg/Bacteria/Xanthomonas/XOO/Xoo_PXO99A/FinalAsm_June2007/AA | Location: /fs/szasmg/Bacteria/Xanthomonas/XOO/Xoo_PXO99A/FinalAsm_June2007/AA | ||
bank2contig Xoo.bnk/ > Xoo.contig | $ bank2contig Xoo.bnk/ > Xoo.contig | ||
grep ^# Xoo.contig | head | $ grep ^# Xoo.contig | head | ||
##1106158952778_stitched 62611 5249768 bases, 00000000 checksum. | ##1106158952778_stitched 62611 5249768 bases, 00000000 checksum. | ||
#XOOB626TF(-939) [] 998 bases, 00000000 checksum. {11 1004} <-938 59> | #XOOB626TF(-939) [] 998 bases, 00000000 checksum. {11 1004} <-938 59> | ||
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#XO1FR06TF(5248815) [] 952 bases, 00000000 checksum. {15 964} <5239123 5240072> | #XO1FR06TF(5248815) [] 952 bases, 00000000 checksum. {15 964} <5239123 5240072> | ||
bank2fasta -b Xoo.bnk/ > Xoo.fasta (5240073 bp , 63.63 GC%) | $ bank2fasta -b Xoo.bnk/ > Xoo.fasta (5240073 bp , 63.63 GC%) | ||
Problem : seq_name's (Ex:XOOB626TF) must be mapped to trace_name's based on the .frg file | Problem : seq_name's (Ex:XOOB626TF) must be mapped to trace_name's based on the .frg file | ||
the .contig file must be updated with trace_name's | the .contig file must be updated with trace_name's | ||
$ convertContig --force-circ 1106158952778_stitched Xoo.translated.contig Xoo.translated.xcontig | |||
Revision as of 17:24, 15 August 2007
XCA : Xanthomonas campestris pv. armoraciae 756C
JCVI NCBI Taxonomy Tax ID: 329463
XOC : Xanthomonas oryzae pv. oryzicola BLS256; draft; NZ_AAQN00000000
JCVI NCBI Taxonomy Tax ID: 129394
XOO : Xanthomonas oryzae pv. oryzae strain PXO99A
JCVI NCBI Taxonomy Tax ID: 360094
NCBI TA: 62,229 traces TA FTP
NCBI AA Location: /fs/szasmg/Bacteria/Xanthomonas/XOO/Xoo_PXO99A/FinalAsm_June2007/AA
$ bank2contig Xoo.bnk/ > Xoo.contig
$ grep ^# Xoo.contig | head
##1106158952778_stitched 62611 5249768 bases, 00000000 checksum.
#XOOB626TF(-939) [] 998 bases, 00000000 checksum. {11 1004} <-938 59>
#XO1EZ18TR(-764) [] 977 bases, 00000000 checksum. {19 993} <-763 213>
...
#XO1C975TF(5248807) [RC] 875 bases, 00000000 checksum. {891 19} <5239115 5239987>
#XO1FR06TF(5248815) [] 952 bases, 00000000 checksum. {15 964} <5239123 5240072>
$ bank2fasta -b Xoo.bnk/ > Xoo.fasta (5240073 bp , 63.63 GC%)
Problem : seq_name's (Ex:XOOB626TF) must be mapped to trace_name's based on the .frg file
the .contig file must be updated with trace_name's
$ convertContig --force-circ 1106158952778_stitched Xoo.translated.contig Xoo.translated.xcontig