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Question: Commandline SAMtools/BEDtools help!
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gravatar for syrez.m
3.0 years ago by
syrez.m • 0
syrez.m • 0 wrote:

Hi all! 

I'm trying to teach myself SAMtools/bedtools commands (on UNIX running on a VM). For practice, I have found a .bam file. I'm trying to find an online source which will show me how to do the following.

How many alignments does the set contain?

How many alignments show the read’s mate unmapped?

How many alignments contain a deletion (D)?

How many alignments show the read’s mate mapped to the same chromosome?

How many alignments are spliced?

Extract only the alignments in the range “Chr?:10,677,300-11,894,100”, corresponding to a locus of interest. 

 

Any help would be greatly appreciated! or even a nod in the right direction. Thanks for reading!
bedtools command line flagstat samtools • 898 views
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modified 3.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.0 years ago by syrez.m • 0
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gravatar for Jennifer Hillman Jackson
3.0 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

If the goal is to duplicate a function in Galaxy, the tool can be executed and then the "View Details" icon clicked on to review the command line used. It looks like this inside a dataset's box in the history panel:

Other than that, manual pages are the best resource for full options (for these and any tools).

Often there will also be various web sites with help/tutorials for command-line tool usage. Just google the tool name with a few keywords for the function.

Best, Jen, Galaxy team
ADD COMMENT • link written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k
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