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.
If you are using windows and you have to work in Linux for your reserach (especially as many researcher said above), there are anther option to solve your purpose. I think, if you are used to with NGS then you should have a linux server that connected with your NGS system so you can call your linux server by your windows system (remote calling). To do this, you need to install WINSCP (for FTP dual mode accessible platform) and Putty (to direct use your linux server as terminal).
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