Results for "Count"
Blogs
BBTools for bioinformatician !
...---------------Reformat.sh Count k-mers/find unknown primers...t That stands for "quality count histogram". Filter S...ch it maps).NOTE: 3 Zero-count lines are suppressed by defau...in=reads.fq out=kmers.txt k=4 count=t display=999 Will produce...2264 days ago
Basic command-line to run BLAST
...in each one? grep -c '^>' cow.1.protein.faa grep -c '^>' human.1.protein.faa This grep command uses the c flag, which reports a count of lines with match to the pa...2237 days ago
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Bookmarks
Public Databases for Bioinformatics !
...mnt/data/ globally accessible data should store common data here e.g. genomes and indexes, annotations, ENCODE data if you dont want this to count towards your quote you must c...1132 days ago
CovCal: Coverage / Read Count Calculator
Coverage / Read Count Calculator Calculate how much sequencing you need to hit a target depth of coverage (or vice versa). Instructions: set the read length/configuration an...2159 days ago
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Files
- Mostly FASTA file contain NNN characters, which can be replace by random A T G C character with this perl script. It also print the FASTA sequence name, N's counts, nucleotide count and percentage details at command prompt/standard output.
3859 days ago
Pages
A guide for complete R beginners :- Getting data into R
...a$B, name=c(“Value A”, “Value B”) , ylab=“Count of Something”) same..., B, name=c(“Value A”, “Value B”) , ylab=“Count of Something”) Scatt...3351 days ago
Frequent words problem solution by Perl
...ct matching kmers with sliding windowmy ($string, $myStr, $kmer)=@_;my $count=0;for (my $aa=0; $aa<=(len...nbsp;#print "$myWin eq $myStr\n"; $count++; }}return...3245 days ago
Top-level pages
Most Commonly used Awk by Bioinformatician
...")>0)l[$1]=$0}$1 in l{print $0"\t"l[$1]}' file2.txt > output.txt count number of occurrence of colum...he first occurrence (uniq): awk '!($2 in l){print;l[$2]=1}' input.txt count different words (wc): awk '{...3905 days ago
Useful Publications and Websites for Deep Sequencing Data Analysis
...ly expressed genes from RNA-seq data. Wang et al., Bioinformatics. 26(1):136-8. 2010 PubMed DEseq: Differential expression analysis for sequence count data. Anders and Huber, Genom...3772 days ago
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Wire posts
Fun
- ...ional biology student was told to write "It is in my gene!!!" on the board 100 times as a punishment. here's his response -use warnings;for ($count=1; $count <=100; $count++) { print "...
3694 days ago
Bio-Scripts
Count the frequency of base G in a given DNA sequence
...trict; use warnings; my $DNA = "GATTACACAT"; #initialize $countG and $currentPos my $countG = 0; my $currentPos = 0;...in the sequence check if it is the base G #if 'yes' increment $countG while($currentPos < $DNAlen...2910 days ago
Perl script to count the number of Adenine, Thymine, Guanine and Cytosine in your DNA Sequence
...ile is:\n $DNA \n"; $DNA =~ s/\s//g; @DNA = split( '', $DNA ); $count_of_A = 0; $count_of_C = 0; $count_of_G = 0;...rs; } } print "Adenine = $count_of_A\n"; print "Cytosine = $count_of_C\n"; print "Guanine = $c...2909 days ago
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Comments
Comment on "Tools for Differential expression analysis"
...a negative binomial distribution to model the count data and provides methods for...t uses a generalized linear model to model the count data and provides methods for...he negative binomial distribution to model the count data and provides methods for...414 days ago
Comment on "Sibelia: A comparative genomics tool"
..., then the are three instances of this block in the input sequence 2. Count -- number of synteny blocks w...e Here is an example of such table from a report file. | Degree | Count | Total | Seq 1 | Seq 2...1278 days ago
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