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smithlabcode / methpipe

A pipeline for analyzing DNA methylation data from bisulfite sequencing.
http://smithlabresearch.org/methpipe
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NULL lines contained in .mr file which transformed from bam file #197

Closed vanessayang0927 closed 2 years ago

vanessayang0927 commented 2 years ago

Hi, I installed version 4.1.1 successfully and prepared to computer methylation entropy. When I used "to-mr" command for transforming bam file to .mr file, it run without error and wrote a .mr file contained many NULL line. However I get the error information "bad line in MappedRead file: (NULL) 0 0 X 0 + " in the next analysis (methstates).

error read information in bam file: DP800003707TRL1C042R0210262385 147 chrM 14387 42 80M = 14473 186 TAATTTTATTAAAATATTTATTAAGATTTTAATTTTTGATTTTTATGTTTTAGGATATTTTTTAATAGTTATTGTTGTAG FFFFGFFFFGFFFFGFFFGFFFFFEFFFFFFFFFFFFF<FF;FFFFFFFFFFFFFFFFFFDFFFFFFFFFFFFFFFFFFF NM:i:0 PG:Z:MarkDuplicates DP800003707TRL1C042R0210262385 99 chrM 14473 42 100M = 14387 -186 TAAAGATAATTATTATTTTTTTTAAATAAATTAAAAAAATTATTAAATTTATATAATTTTTTTTAAAATTTAGAATAATAATATATTTGATTATATTGTT FGFFFFFFFFFFFEGGFFF9FFFGFFFGFGFFGFFFFGFEFGFG?;GGFEEGEFGDCFGFGGFAGFGGGCGDFFFAFBFGGEF?EG<GFAFFDF6GGFG= NM:i:0 PG:Z:MarkDuplicates

guilhermesena1 commented 2 years ago

Hello,

Thank you for reaching out about the problem. This issue was fixed on methpipe 5.0.0 (along with several other improvements in the pipeline). Would you be able to analyze your data with that instead? You would not need to use to-mr and can instead directly use the output of the mapper you are currently using.

vanessayang0927 commented 2 years ago

Thank you for your reply. I installed version 5.0.0 successfully and run without error. However, the entropy values of all CpG sites were negative. Was this normal?

guilhermesena1 commented 2 years ago

Closing this to discuss on another issue. If there are still problems with the 5.0.0 version conversion this issue can be re-opened and we can discuss here.