(Warning message: total noob talking)
Hello all,
I know nothing about sequencing or sequences alignment.
I was given a collection of short reads (millions of them) and I would like to map them to the mouse genome and to visualize the surrounding sequence and the alignment (and do some kind of quantification of expression, maybe...).
I have no clue on how to do this and started looking around for some software that would help me (I won't blast millions of reads one by one, right?).
However, I found most of the software to be CLI-based. In addition to my total lack of experience in sequencing and sequence handling, I'm not very comfortable with the terminal neither and I fear I would not understand the output of such programs.
I am thus looking for a GUI-based software (any platform is OK, mac would be my favorite choice) in order to allow me to visualize where all these reads map in the mouse genome.
I am ready to read tons of manual pages and tutorial if necessary but, again, I am a bit allergic to the terminal. I mean, if the software is CLI-based but the output is something easy to understand (like a zoomable image, in my dreams) I would go for it.
Tell me if you guys know any tool that could help me (or a better way to answer my questions).
Thank you very much in advance for your help.
Best regards
-a-
Hello all,
I know nothing about sequencing or sequences alignment.
I was given a collection of short reads (millions of them) and I would like to map them to the mouse genome and to visualize the surrounding sequence and the alignment (and do some kind of quantification of expression, maybe...).
I have no clue on how to do this and started looking around for some software that would help me (I won't blast millions of reads one by one, right?).
However, I found most of the software to be CLI-based. In addition to my total lack of experience in sequencing and sequence handling, I'm not very comfortable with the terminal neither and I fear I would not understand the output of such programs.
I am thus looking for a GUI-based software (any platform is OK, mac would be my favorite choice) in order to allow me to visualize where all these reads map in the mouse genome.
I am ready to read tons of manual pages and tutorial if necessary but, again, I am a bit allergic to the terminal. I mean, if the software is CLI-based but the output is something easy to understand (like a zoomable image, in my dreams) I would go for it.
Tell me if you guys know any tool that could help me (or a better way to answer my questions).
Thank you very much in advance for your help.
Best regards
-a-
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