Hey everybody,
I search a tool to compute the max depth of a feature (e.g. exon, gene)
For example:
I have a feature and three reads. the Two reads overlaps a base or three reads overlaps another base. Now I want the max depth of the base. Here in the example is the max depth three.
Is there a tool to get this values?
Thank you for your help.
i've written BamStats04 http://lindenb.github.io/jvarkit/BamStats04.html
$ java -jar dist/bamstats04.jar \
-B data.bed \
f.bam
#chrom start end length mincov maxcov mean nocoveragebp percentcovered
1 429665 429785 120 42 105 72.36666666666666 0 100
1 430108 430144 36 9 9 9.0 0 100
1 439811 439904 93 0 36 3.6451612903225805 21 77
1 550198 550246 48 1325 1358 1344.4583333333333 0 100
1 629855 629906 51 223 520 420.70588235294116 0 100
1 689960 690029 69 926 1413 1248.9420289855072 0 100
1 690852 690972 120 126 193 171.24166666666667 0 100
1 787283 787406 123 212 489 333.9756097560976 0 100
1 789740 789877 137 245 688 528.6715328467153 0 1
Hey Pierre,
i try your tip. I search currently a tool thats calculate the value e.g. in MACS2 the pileup value in the results. Which means how many fragments you can find covering the peak summit. And I want the max coverage of a base for every single feature(e.g. exon). For example depth 5x is the maximum. The problem in bedtools coverage is, that only calculate the depth for each single base, but not the max depth of single base.
And I want the max coverage of a base for every single feature(e.g. exon). For example depth 5x is the maximum. The problem in bedtools coverage is, that only calculate the depth for each single base, but not the max depth of single base.
I don't understand. Show an input and the corresponding output.
my tool has a 'maxcov' column. What is missing ?
if it works, click on the green tick on the left to close the question
You can try HTSeq. Check-out the different modes available.
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Check out bam-readcount if you need base level statistics.
For feature level summaries featureCounts or HTSeq-count noted below are good options.
BTW: Requirements in the title of your post (feature level) and the description in the body (base level summary) are not matching.
thank all for your answers.
Currently i search a tool that compute the pileup value as in MACS2. Which means how many fragments you can find covering the peak summit. But I don't finde a tool where I get the highest covering value for a feature. I try to use BamStats04 .. the tip from Pierre .
Thanks
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