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| | colspan="2"| | | | colspan="2"| |
| <!-- ##### DO NOT edit above this line unless you know what you are doing. ##### --> | | <!-- ##### DO NOT edit above this line unless you know what you are doing. ##### --> |
| ==Mapping alignments to barcodes using command line BLAST==
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|
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| '''BLAST command line manual:'''
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| http://www.ncbi.nlm.nih.gov/books/NBK1763/
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|
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| '''BLAST command line dmg for Mac:'''
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| ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.2.25+.dmg
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|
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| '''samtools call for viewing .bam:'''
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| samtools view filename.bam > filename.sam
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| note: this can also be piped to awk, etc. for parsing
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|
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| '''UNIX command to convert sam to fasta using awk'''
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| awk '{OFS="\t"; print ">"$1"\n"$10}' filename.sam > filename.fa
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|
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| '''command line call to generate indexed reference files for mapping to:'''
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| makeblastdb -in reference.fa -dbtype nucl -parse_seqids -out reference.fa -title "Reference_Title"
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|
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| '''command line blastn call:'''
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| 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
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|
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| '''R script for summarizing data:'''
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| [~/Work/BLAST/BLAST_parsing.R BLAST_parsing.R]
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|
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| <!-- ##### DO NOT edit below this line unless you know what you are doing. ##### -->
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| |}
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|
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| __NOTOC__
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