Sam:LabNotes/Microbiome-new/2011-4-14: Difference between revisions
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>Sam Chiang |
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samchiang@genemapster:~/Tools/blatSuite34_64$ ./blat -out=blast /media/disk-1/samchiang/Raw-Read-Complete/101123_HL083/HC-MDA-Ecoli-SAGs-Ind1to8-SE/failed-or-nonspecific/s_4_ID1.failed.fa /media/disk-2/samchiang/Tools/bowtie-0.12.5/genomes/e_coli_k12_mg1655.fasta /media/disk-1/samchiang/Sub_tests_folder_imp/3_Quantify_lowquality_reads_Ecoli_SAGs/HL083_Ecoli_SAG_ID1.failed.fa.BLAT.txt & | samchiang@genemapster:~/Tools/blatSuite34_64$ ./blat -out=blast /media/disk-1/samchiang/Raw-Read-Complete/101123_HL083/HC-MDA-Ecoli-SAGs-Ind1to8-SE/failed-or-nonspecific/s_4_ID1.failed.fa /media/disk-2/samchiang/Tools/bowtie-0.12.5/genomes/e_coli_k12_mg1655.fasta /media/disk-1/samchiang/Sub_tests_folder_imp/3_Quantify_lowquality_reads_Ecoli_SAGs/HL083_Ecoli_SAG_ID1.failed.fa.BLAT.txt & | ||
*Results | |||
**It is unclear why but The BLAT result (in BLAST output format) doesn't contain any header-string information. So MEGAN can't identify taxonomic information from BLAT results. | |||
**I did several tests and confirm that it's not due to the output format (blast or .psl) I chose. It's probably due to that the reference genome is a one string FASTA file. |
Revision as of 08:14, 18 April 2011
Quantify low quality E.coli reads from Ecoli SAGs sequencing results
Background
- Since bowtie mapping is very stringent, some E.coli reads (assuming they are low-quality E.coli reads) are not able to be mapped.
- Total reads = mappled E.coli reads + non-mapped E.coli reads + non-mapped non-E.coli reads
- The objective here is to quantify how many of those non-mapped E.coli reads.
- We can't not directly BLASTN all of the failed-to-align reads since it will take extremely long time (> 1 week) using genemapster.
Possible approaches
Test1: BLATing failed-to-align reads
- BLAT failed-to-align reads to E.coli genome -> output in BLAST-output format -> MEGAN extraction of E.coli related reads and get quantitative information.
- Since the failed-to-aling reads (e.g. s_4_ID1.failed) are FASTQ file, I need to trasform them to FASTA files before I can BLAT them.
- Using script fastq2fasta-hc.pl to transfer FASTQ format to FASTA format
BLAT command: samchiang@genemapster:~/Tools/blatSuite34_64$ ./blat -out=blast /media/disk-1/samchiang/Raw-Read-Complete/101123_HL083/HC-MDA-Ecoli-SAGs-Ind1to8-SE/failed-or-nonspecific/s_4_ID1.failed.fa /media/disk-2/samchiang/Tools/bowtie-0.12.5/genomes/e_coli_k12_mg1655.fasta /media/disk-1/samchiang/Sub_tests_folder_imp/3_Quantify_lowquality_reads_Ecoli_SAGs/HL083_Ecoli_SAG_ID1.failed.fa.BLAT.txt &
- Results
- It is unclear why but The BLAT result (in BLAST output format) doesn't contain any header-string information. So MEGAN can't identify taxonomic information from BLAT results.
- I did several tests and confirm that it's not due to the output format (blast or .psl) I chose. It's probably due to that the reference genome is a one string FASTA file.