Results for "sam"
Top-level pages
List of Bioinformatics Software Tools for Next Generation Sequencing
...Takes NGS data (.fastq, BAM, SAM), microarrays (Affymetrix, Il...t used for analysis of single samples; implemented in C and use...ntegrates read tallies to the sample level and to the tumor-nor...lone program, uses “the same feature set and training dat...2907 days ago
- ...tools, currently bundled with SAMtools, for identifying and fil...ic genotype is present in the sample of interest. Genotype like...uery Name). Used in FASTQ and SAM files. paired-end sequencing...line utility decodes a single SAM flag value into plain English...
2867 days ago
Genome Assembly Tools and Software - PART1 !!
.... Third, non-redundant sequences matched to the same gene of reference genome are...diploid genomes, and genomes from environmental samples. Celera Assembler contrib...as obtained from bulk sequencing of mixed virus samples. TAG 0.91 – Tr...2684 days ago
- To do sam to bam conversion, follow the following commands :- Code: $ samtools view -b -S file.sam > file.bam Then you wil...file.bam file-sorted followed by Code: $ samtools index file-sorted.bam...
2289 days ago
Some useful Bioinformatics links
...b#fig4 How to determine chimeras in my de novo assembly? - SEQanswers http://seqanswers.com/forums/showthread.php?t=26721 samtools(1) manual page http://www.htslib.org/doc/samtools.html How To Filter Mappe...2240 days ago
- ...done To split bam files into sets with mapped and unmapped reads: samtools view -F4 sample.bam > sample.mapped.sam...!first){first=$5;}; last=$5;} END {print last-first}' myfile.txt To sample only 200 first bases from...
2215 days ago
Frequent Paired-end reads (PE 2x100) mapping command lines
...-q -1 r1.fq -2 r2.fq -S r12.bowtie2.sam bwa aln hs37m.fa r1.fq &...> r2.sai \ && bwa sampe hs37m r1.sai r2.sai r1.fq r.../bwa/hs37m.fa r12.fq > r12.bwasw.sam gsnap -A sam -d hs37m r1....py -g hs37m -h hs37m -o r12.stampy.sam -M r1.fq,r2.fq soap -D h...2180 days ago
A quick guide to Phred scaling
...xamples:• 90% confidence (10% error rate) = Q10• 99% confidence (1% error rate) = Q20• 99.9% confidence (.1% error rate) = Q30• SAM encoding adds 33 to the value...1532 days ago
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