Samtools does have an option to filter the reads according to regions specified in the BED format but it will not automatically annotate them. You can use any scripting language like awk or perl to parse. See this link for the details on the SAM format. What I would do is convert the BAM to SAM (using samtools) or to BED (using bedtools: bamtobed) and parse the columns of the SAM/ BED file describing the read locations with the GTF file. I don't have much experience with this tool. You can obtain the association between genomic locations and the reads using the BEDOPS toolkit as mentioned in this Biostars post. The annotations are available in the form of GTF/GFF files. This information is not available unless you have the genome annotations.
You want to know, to which genes do these reads map to. Since you already have the alignments ( aln.bam) to hg19, you do not need to perform alignment. Again, there are many aligners available Bowtie, STAR and now a new one called HISAT. trims dirty ends from sequence files based on ambiguity in the pherogram, performs heterozygote. Then you have to align your trimmed reads to a reference, using an aligner. SEQUENCHER - Analysis of automated sequence files. large number of undetermined characters appear at both ends of a sequence S. You can find the adaptor composition of each read by subtracting the read length post trimming from the read length pre-trimming (this would be same for all reads). Sequencher 5.0 17 (a commercial product by Gene Codes) is more similar to. You can get to know the adaptor sequence by running FastQC. FastQC is for analysing the read qualities and average composition. Samtools is not an aligner it is used to analyse alignments.
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