Sam:LabNotes/Microbiome-new/2011-4-19: Difference between revisions

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>Sam Chiang
(Created page with '='''Recruit metagenomic contigs using mouse SAG contigs as baits - BLATing approach'''= ==Objective== *Extract more contigs from metagenomic data into mouse GI microbiome SAG da…')
 
>Sam Chiang
Line 7: Line 7:
==Background==
==Background==
*I did BLATing test and found that BLAT can working either 1 string reference genome or multiple sequence references.
*I did BLATing test and found that BLAT can working either 1 string reference genome or multiple sequence references.
*We The pre
*Stringency test:
**I BLAT metagenomic contigs(query) against SAG contigs (reference). I pick up four BLAT results for alignment analysis. Two of queries aligned to reference template at 40~50%, which suggest the default BLAT stringency is suitable for our recruiting purpose.
 
==Procedures==
===BLATing metagenomic contigs against mouse SAG contigs===
*Query: Mouse metagenomic contigs(HC9, HC10, HC11, HC12)- assembled by Dr. Zhang (soapK27M3)
*Target: Mouse SAGs contigs batch A (ID1 ~ ID12) - assembled by Dr. Zhang (soapK27M3)
Command:
e.g.
samchiang@genemapster:~/Tools/blatSuite34$ ./blat -out=psl /media/disk-2/samchiang/Raw-Read-backup/Bigelow_MouseSAG/kz_SOAP_denovo/MmSAG_BatchA_HL081_s6-8/s6-8_A_ID1.contig.100up /media/disk-2/samchiang/Raw-Read-backup/Bigelow_MouseSAG/kz_SOAP_denovo/Mm_Matagenom_HL087_s5-8/HC10_RLV.Soap.K27M3.contig.100up /media/disk-2/samchiang/Analysis_output/BLAT_Meta2SAG_040311/Reg_BLAT_HC10_to_SAG_A_ID1 &

Revision as of 06:54, 20 April 2011

Recruit metagenomic contigs using mouse SAG contigs as baits - BLATing approach

Objective

  • Extract more contigs from metagenomic data into mouse GI microbiome SAG data.
  • If this approach is working, the increased data amount will help us to extend SAG contig length and build up genome of unknown bacteria.

Background

  • I did BLATing test and found that BLAT can working either 1 string reference genome or multiple sequence references.
  • Stringency test:
    • I BLAT metagenomic contigs(query) against SAG contigs (reference). I pick up four BLAT results for alignment analysis. Two of queries aligned to reference template at 40~50%, which suggest the default BLAT stringency is suitable for our recruiting purpose.

Procedures

BLATing metagenomic contigs against mouse SAG contigs

  • Query: Mouse metagenomic contigs(HC9, HC10, HC11, HC12)- assembled by Dr. Zhang (soapK27M3)
  • Target: Mouse SAGs contigs batch A (ID1 ~ ID12) - assembled by Dr. Zhang (soapK27M3)
Command:
e.g. 
samchiang@genemapster:~/Tools/blatSuite34$ ./blat -out=psl /media/disk-2/samchiang/Raw-Read-backup/Bigelow_MouseSAG/kz_SOAP_denovo/MmSAG_BatchA_HL081_s6-8/s6-8_A_ID1.contig.100up /media/disk-2/samchiang/Raw-Read-backup/Bigelow_MouseSAG/kz_SOAP_denovo/Mm_Matagenom_HL087_s5-8/HC10_RLV.Soap.K27M3.contig.100up /media/disk-2/samchiang/Analysis_output/BLAT_Meta2SAG_040311/Reg_BLAT_HC10_to_SAG_A_ID1 &