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Generate size histograms from alignment files (version 0.9.9)

Will you select a reference genome from your history or use a built-in index?:

Built-ins were indexed using default options

Add alignment files

Add alignment files 0

Optional: select a GFF to investigate regions of interest:

GFF must match genome build

Generate size distribution for each item, or generate a global alignment:

Whether + and - reads should be collapsed or not:

Min size of reads to plot:

'15' = 15 nucleotides

Max size of reads to plot:

'30' = 30 nucleotides

Main Titles:

x axis label:

y axis label:

y axis range for size distributions. 0 means auto-scaling.:

How many items to display per page?:

What it does

Takes one or more alignment files (BAM, SAM or tabular bowtie output) as input and produces a histogram of read sizes, where by default for each "chromosome" a histogram of read sizes is drawn. Reads that map in sense are on the top (red), reads that map antisense are on the bottom (blue).

'''TIP''' The input data can be produced using the sRbowtie tool.

'''Example'''

Query sequence:: For a SAM file as the following:

5 16 2L_79 24393 255 17M * 0 0 CCTTCATCTTTTTTTTT IIIIIIIIIIIIIIIII XA:i:0 MD:Z:17 NM:i:0

11 0 2R_1 12675 255 21M * 0 0 AAAAAAAACGCGTCCTTGTGC IIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:21 NM:i:0

2 16 2L_5 669 255 23M * 0 0 TGTTGCTGCATTTCTTTTTTTTT IIIIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:23 NM:i:0

produce a plot like this:

/repository/static/images/524a81a74d545d79/static%2Fimages%2Fsize_histogram.png