Regarding Bamstat05 output

Question

[DL]

Hello,

I ran bamstats05 to check the coverage from bam file. Can anyone explain the output of bamstat5. it seems quite simple but i want to confirm description of output. i do not understand here whats the exactly meaning of mincov, maxcov and avg ???

Here is the output:

#chrom  start   end gene    sample  length  mincov  maxcov  avg nocoverage.bp   percentcovered
Chr01   3228    3401    RC1G0000100 1003    173 0   21  7.728323699 47  72
Chr01   57184   59741   RC1G0000200 1003    2557    0   388 87.05044975 14  99
Chr01   70350   70611   RC1G0000300 1003    261 0   17  7.513409962 108 58
Chr01   83214   86140   RC1G0000400 1003    2926    0   17  0.858168148 2354    19
Chr01   119712  120235  RC1G0000500 1003    523 0   37  15.30592734 4   99

Thanks in advance

[finswimmer]

Hello DL,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!

[DL]

Ok, i will remember next time.

Thank you

Answer 1

[finswimmer]

Hello DL,

mincov is the minimum coverage at at least one position within the the given interval. Therefor maxcov is the maximum coverage on at least one position. And average - well - is the mean coverage within the given intervall.

fin swimmer

[DL]

Thank you for your reply. If i understand well then coverage is depth that mention how many reads are aligned at that particular position and in my table it showed zero. Its mean that no reads are aligned at some positions.

Thank you

[finswimmer]

If i understand well then coverage is depth that mention how many reads are aligned at that particular position

It depends :) You may have a look into the manual for it. Before calculating the coverage there might be some filtering steps, e.g. don't count duplicates, don't count reads with a mapping quality below a given treshold, ... Also it should clearly stated out what happens if you have paired end reads which overlap. Do we count this as 1 (it should be!) or as 2?

in my table it showed zero. Its mean that no reads are aligned at some positions.

Yes, have a look at the column nocoverage.bp. There you see how many bases are not covered by any read.

fin swimmer

[DL]

Thank you for your reply .

Regards

[Pierre Lindenbaum]

Its mean that no reads are aligned at some positions.

Its mean that no reads, passing the filters (see the option -f), are aligned at some positions.

[DL]

Thank you for your reply. I see -f option but i did not understand how can i run command with -f option if i want to take only those reads that mapped less than 10 times. because i want to calculate coverage mapped reads on transposable elements so i gave bed file for TE and bam file after mapping but i think that because of repetitive region one read can align so many places. So can you please tell me how can i run command with -f option.

Thanks

[Pierre Lindenbaum]

want to take only those reads that mapped less than 10 times.

that's another question : You'll have to filter your bam first to keep " the read mapped less than 10 times"