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chhylp123 / BitMapperBS

BitMapperBS: a fast and accurate read aligner for whole-genome bisulfite sequencing
Apache License 2.0
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Anytools that can replace MethylDackel ? #15

Closed zorrodong closed 5 years ago

zorrodong commented 5 years ago

Thanks for the wonderful tool to handle methylation datasets.

Since I have several problems when using MethylDackel, I wonder are there any other recommended tools to deal with the generated bam files?

Thank you very much and looking forward to your reply!

Best wishes,

Zorro 20190620

chhylp123 commented 5 years ago

Hi Zorro,

I also found MethylExtract (https://bioinfo2.ugr.es/MethylExtract/index.html). But I haven't test it so I cannot make sure if it works well. In addition, BitMapperBS has its own methylation extract part. If you want to try, I can add docs for it. But please note that the methylation extract part of BitMapperBS does not use bam file. So maybe you cannot control the quality of the results by utilizing samtools.

BTW, may I ask what's the problem of MethylDackel? Maybe I can help you to solve them. I will make the methylation extract part of BitMapperBS better next week. But I'm busy this week to move to a new lab. So if you need BitMapperBS urgently, I still recommend MethylDackel.

Thanks a lot.

Thanks for the wonderful tool to handle methylation datasets.

Since I have several problems when using MethylDackel, I wonder are there any other recommended tools to deal with the generated bam files?

Thank you very much and looking forward to your reply!

Best wishes,

Zorro 20190620

zorrodong commented 5 years ago

Thanks for the reply! Now I have it done successfully. Previously I lacked some libs.

Best wishes,

Zorro

zorrodong commented 5 years ago

Sorry to bother you again.

I wonder whether I can extract the ummaped pair-end reads in to a fastq file, and perform the single-end mapping mode?

I find it will improve the mapping rate a little bit. Do you have any comments on this pipeline?

Looking forward to your reply!

Best wishes,

Zorro 20190622

chhylp123 commented 5 years ago

I can add this feature in BitMapperBS this weekend. But I think mapping the unmapped PE reads in single-end mode may result incorrect alignment results. I’m not sure.

Sorry to bother you again.

I wonder whether I can extract the ummaped pair-end reads in to a fastq file, and perform the single-end mapping mode?

I find it will improve the mapping rate a little bit. Do you have any comments on this pipeline?

Looking forward to your reply!

Best wishes,

Zorro 20190622

chhylp123 commented 5 years ago

Sorry for late reply.

You can try the option '--unmapped_out'. With '--unmapped_out', the unmapped reads would be outputted to BAM file. After that, you can extract fastq from the BAM. Thanks.

Sorry to bother you again.

I wonder whether I can extract the ummaped pair-end reads in to a fastq file, and perform the single-end mapping mode?

I find it will improve the mapping rate a little bit. Do you have any comments on this pipeline?

Looking forward to your reply!

Best wishes,

Zorro 20190622

zorrodong commented 5 years ago

Yeah, I have already done so.

Thanks very much!