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cat Uame-Purple-merged.list.txt | cut -f 2,3 | sed 's,|,\t,g' | cut -f 2,4 | nsort -u | cut -f1 | nsort | uniq -c

setwd ('/data/project/flowers/orthologous/transcriptional_factors') lista1 <- read.delim(file='TFs.list', header=F, stringsAsFactors=F) lista2 <- read.delim(file='PlantTFDB-allxUame-Purple_assm_id60_moresensitive_cov60', header=F, stringsAsFactors=F) colnames(lista1) <- c('ID', 'Desc') colnames(lista2) <- c('Transcript', 'ID', 'pident', 'length', 'mismatch', 'gapopen', 'qstart', 'qend', 'sstart', 'send', 'evalue', 'bitscore') head (lista1) head (lista2) merged_list <-  merge(x=lista1, y=lista2, by.x='ID', by.y='ID') head (merged_list) dim(merged_list) library(xlsx) #write.xlsx(merged_list, 'Uame-Purple-merged.list.xls') write.table(merged_list, file='Uame-Purple-merged.list.txt', row.names=F, col.names=T, quote=F, sep="\t")

retirado de : http://www.peter.unmack.net/molecular/programs/paup.command.blocks.html Common PAUP analysis commands By Peter Unmack I usually paste the blocks below to the end of my nexus files, open the command line version (which runs faster than the GUI) and execute the file (I usually copy the datafile to my paup directory, or copy paup to where my datafile is).   Stuff highlighted in yellow is what usually gets changed by the user depending upon their dataset and needs. Parsimony Analysis begin paup; set autoclose=yes; set criterion=parsimony; set root=outgroup; set storebrlens=yes; set increase=auto; outgroup fish1 fish2 etc ; hsearch addseq=random nreps=1000 swap=tbr hold=1; savetrees file= datasetname .cb.pa.tree.nex format=altnex brlens=yes; pscores /tl ci ri rc; end; Parsimony Bootstrap Analysis begin paup; set autoclose=yes; set criterion=parsimony; set root=outgroup; set storebrlens=yes; set increase=auto; outgr...

retirado de : https://www.biostars.org/p/56246/ Hi, You get a bam (machine readable sam ) file after mapping, and it contains information about mapped and unmapped reads. To get the unmapped reads from a bam file use : samtools view -f 4 file.bam > unmapped.sam , the output will be in sam to get the output in bam use : samtools view -b -f 4 file.bam > unmapped.bam To get only the mapped reads use the parameter 'F', which works like -v of grep and skips the alignments for a specific flag. samtools view -b -F 4 file.bam > mapped.bam From the manual ; there are different int codes you can use with the parameter 'f', based on what you want : -f INT Only output alignments with all bits in INT present in the FLAG field. INT can be in hex in the format of /^0x[0-9A-F]+/ [0] Each bit in the FLAG field is defined as: Flag Chr Description 0x0001 p the read is paired in sequencing 0x0002 P the...

https://broadinstitute.github.io/picard/explain-flags.html

Sam format: column information: QNAME: Query name of the read or the read pair FLAG: Bitwise flag (pairing, strand, mate strand, etc.) RNAME: Reference sequence name POS: 1-Based leftmost position of clipped alignment MAPQ: Mapping quality (Phred-scaled) CIGAR: Extended CIGAR string (operations: MIDNSHP) MRNM: Mate reference name (‘=’ if same as RNAME) MPOS: 1-based leftmost mate position ISIZE: Inferred insert size SEQQuery: Sequence on the same strand as the reference QUAL: Query quality (ASCII-33=Phred base quality) FURTHER DETAILS OF SAM FORMAT: http://samtools.sourceforge.net/SAM1.pdf

 https://phylogeneticgeek.wordpress.com/2011/09/16/how-to-run-paup-in-mac-os-x-tiger-under-classic-environment/   How to run PAUP in Mac OS X Tiger (under classic environment) September 16, 2011             1 Vote PAUP * 4.0 (Phylogenetic Analysis Using Parsimony (and Other Methods)) is a popular phylogenetic software.  If you’re in this field of work, you’ve likely have used it or have at least heard of it before.  If you want to use PAUP and you have an Intel Mac, you’ll have to resort to the command line version of the program.  This is because the GUI (Graphical User Interface) version of PAUP only runs in older Macs with PPC processors (i.e. G3, G4, G5). The nice thing about GUI version of PAUP is you can print your trees as a PICT file and you can import it into Word and other Adobe programs to edit it and polish it for a publication.  In the GUI version, it is much eas...