dears: I'm working on chip-seq data. I've downloaded sra format data. to analyze I have to convert them to fastq format and then to SAM file. I made a fastq file but I cant convert it to SAM file? who knows how I can do this?
fastq is a file that store raw sequence and quality scores. sam is a file that store mapped tags to genome. You can not "convert" a fastq file into a sam, but you have to map the sequences in the fastq to the reference genome to obtain a sam output. I normally use bowtie to do it:
bowtie --best --strata -m1 --sam -l 36 -n 3 h_sapiens_ncbi36 -q SAMPLE.fastq > SAMPLE.sam
Hope this help
best
r
fastq is a file that store raw sequence and quality scores. sam is a file that store mapped tags to genome. You can not "convert" a fastq file into a sam, but you have to map the sequences in the fastq to the reference genome to obtain a sam output. I normally use bowtie to do it:
bowtie --best --strata -m1 --sam -l 36 -n 3 h_sapiens_ncbi36 -q SAMPLE.fastq > SAMPLE.sam
Hope this help
best
r
You should map the .fastq file to genome or transcriptome by NGS mapping tools, such as BWA, TopHat....
http://picard.sourceforge.net/command-line-overview.shtml#FastqToSam
This Link may helpful for you.
dears: I've searched these tools. but unfortunately these tools are qualified for Linux. I work with windows 7. what should I do?
If you work with Windows and your research involves NGS, it's time to move to Linux... On second thought, if you work with Windows it's time to move to Linux. :)
You can try using Cygwin, to get Linux like environment for windows. I have never tried it myself, hope it works for you. But I completely agree with Gustavo, if you are working with NGS data, it's time you swtiched to Linux.
You can also use Galaxy https://main.g2.bx.psu.edu/
Saves you from buying a supercomputer :)
definitively you should move to linux. In case of small analysis (or training) you can install VirtualBox and try a fully operative Linux system (Ubuntu-Fedora) without leaving Windows. When you feel the advantages just do it! Jump to the new world!
Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) alignes reads (FastQ/FasrA file) against a reference genome and it has a Windows command-liine executable.
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