Modification summary per BED line

[davidsilvapires]

Hi everybody.

We have a bed file with about 1000 features (one per line) that we are interested in obtaining the number of modified bases per feature (normalized to coverage, preferentially).

Is there any modkit sub-command similar to "summary" to get this kind of result?

Thanks in advance for any help.

--
David

[ArtRand]

Hello @davidsilvapires,

There isn't a command exactly like that. Although I've gotten a similar request before - so maybe it's time to add one.

[davidsilvapires]

Thank you for the answer @ArtRand.

While the subcommand is not implemented, I am using the <() Bash syntax to make use of modkit summary running one BED line each time. Maybe it can be useful to other users:

IFS='
'

for LINE in `cat features.bed`
do
     echo
     echo "${LINE}"
     modkit summary --include-bed <(echo ${LINE}) sample.modBam
done

Here are two output examples:

PRFA01000001    1129695 1129767 C4B63_1nc1      tRNA    -
# bases             C
# total_reads_used  17
# count_reads_C     17
# pass_threshold_C  0.6507813
 base  code  pass_count  pass_frac   all_count  all_frac
 C     -     91          0.9009901   95         0.84070796
 C     m     4           0.03960396  6          0.053097345
 C     h     6           0.05940594  12         0.10619469

PRFA01000005    770166  770238  C4B63_5nc4      tRNA    -
# bases             C
# total_reads_used  12
# count_reads_C     12
# pass_threshold_C  0.74921876
 base  code  pass_count  pass_frac   all_count  all_frac
 C     -     70          0.93333334  76         0.9047619
 C     h     5           0.06666667  7          0.083333336
 C     m     0           0           0          0

Best regards.

--
David