User:Alex S. Nord/Notebook/Computational Work/2011/10/19: Difference between revisions
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'''R script for summarizing data:''' | '''R script for summarizing data:''' | ||
BLAST_parsing.R | BLAST_parsing.R | ||
~/Work/BLAST/BLAST_parsing.R | |||
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Revision as of 12:36, 19 October 2011
 Project name
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<html><img src="/images/9/94/Report.png" border="0" /></html> Main project page |
Mapping alignments to barcodes using command line BLASTBLAST command line manual: http://www.ncbi.nlm.nih.gov/books/NBK1763/ BLAST command line dmg for Mac: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.2.25+.dmg samtools call for viewing .bam: samtools view filename.bam > filename.sam note: this can also be piped to awk, etc. for parsing UNIX command to convert sam to fasta using awk awk '{OFS="\t"; print ">"$1"\n"$10}' filename.sam > filename.fa command line call to generate indexed reference files for mapping to: makeblastdb -in reference.fa -dbtype nucl -parse_seqids -out reference.fa -title "Reference_Title" command line blastn call: blastn -task 'blastn-short' -query query.fa -db reference_index.fa -outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qseq sseq' -max_target_seqs 1 -reward 2 -gapopen 4 > output.txt R script for summarizing data: BLAST_parsing.R ~/Work/BLAST/BLAST_parsing.R | |
