read depth of a feature (e.g gene or exon)

Question

[xd_d]

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.

[GenoMax]

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.

[xd_d]

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

[GenoMax]

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

Answer 1

[Pierre Lindenbaum]

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

[xd_d]

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.

[Pierre Lindenbaum]

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.

[xd_d]

I mean this value for every feature

[Pierre Lindenbaum]

my tool has a 'maxcov' column. What is missing ?

[xd_d]

i tested that and its work, thanks : )

[Pierre Lindenbaum]

if it works, click on the green tick on the left to close the question

Answer 2

[lakhujanivijay]

You can try HTSeq. Check-out the different modes available.