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wangna62691 / PacBio_Assembly

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PacBio SMRTAnalysis Lab IV #4

Open wangna62691 opened 7 years ago

wangna62691 commented 7 years ago

• Develop your modification and motif analysis script and XML files in GitHub, and in a new issue on GitHub • record link to modification and motif script https://github.com/wangna62691/PacBio_Assembly/blob/master/Motif_ecoli.sh

• record exact command used to submit job

qsub -q rcc-30d -l mem_total=8g -pe thread 4 ./Motif_ecoli.sh

• record GitHub revision of script used https://github.com/wangna62691/PacBio_Assembly/blob/371ba5f1ddb249c68815d529b2448e3d1cd8caf8/Motif_ecoli.sh

• report any sequence motifs that are modified at a very high frequency (where >95% of sites for a motif are modified) in the E. coli K12 substr. MG1655 reference genome.

The three motifs are GCACNNNNNNGTT, AACNNNNNNGTGC, GATC. Here are the results from motif_summary.html: Motif Modified Position Modification Type % Motifs Detected
GCACNNNNNNGTT 3 m6A 99.66 AACNNNNNNGTGC 2 m6A 98.32 GATC 2 m6A 98.50

cbergman commented 7 years ago

Excellent, everything is correct and complete. Nice work!