Issue with ModKit DMR Analysis (m6A)

[zine-el-aabidine]

Hi,

I ran modkit pileup --modified-bases m6A to generate bedMethyl files.
I then compressed these files with bgzip and generated the corresponding .tbi index.

I used them in modkit dmr pair -m A --min-valid-coverage 10, but I encountered the following error:

**> batch failed: invalid data, valid coverage (191) is not equal to the sum of canonical and modified counts (190), [BedMethylLine { chrom: "2L", interval: Interval { start: 69060, stop: 69061, val: () }, raw_mod_code: Code('a'), strand: Positive, count_methylated: 0, valid_coverage: 191, count_canonical: 190, count_other: 1, count_delete: 4, count_fail: 15, count_diff: 0, count_nocall: 0 }] chrom: 2L starting at 69060, stopping

failed to send on channel, sending on a disconnected channel
encountered error whilst processing, stopping
Error! invalid-bedmethyl-data**

Could you please advise on what might be causing this issue and how to resolve it?

Thank you in advance for your help.

Best regards,
Amal

[ArtRand]

Hello @zine-el-aabidine,

Could you tell me which model you used for base modification detection and/or what the output of

> modkit modbam check-tags $bam --head 100

is? Thank you.

[zine-el-aabidine]

Thank you for your response, and please accept my apologies for the delay — I was out of the office.

The command returned the following result:

checking tags on first 100 reads

no errors
num PASS records: 100 (100.00%)
num records: 100
valid record tag headers:
+------------+-------+
| tag_header | count |
+------------+-------+
| A+17596. | 100 |
| A+a. | 100 |
| C+m. | 100 |
| T+17802. | 100 |
+------------+-------+

modified bases:
+--------+--------------+----------+------+
| strand | primary_base | mod_code | mode |
+--------+--------------+----------+------+
| + | T | 17802 | . |
| + | C | m | . |
| + | A | 17596 | . |
| + | A | a | . |
+--------+--------------+----------+------+

Thank you again

Best regards

Amal