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Weeks-UNC / shapemapper2

Public repository for ShapeMapper 2 releases
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Read issue with SRA data from GEO Accession GSM3994935 #13

Closed afafbioinfo closed 4 years ago

afafbioinfo commented 4 years ago

SRA files: SRR9878467 (modified) and SRR9878469 (untreated) were used to generate Fastq files R1 and R2 via the command fastq-dump with -I --split-files as option.

SHAPEMapper was run with the following options: --target addcasette.fa --modified --R1 SRR9878467-1.fastq --R2 SRR9878467-2.fastq --untreated --R1 SRR9878469-1.fastq --R2 SRR9878469-2.fastq --radom-primer-len 9

Several reads could not be considered in the SHAPEmapper Analysis, for instance: Warning: skipping read 'SRR9878469.244370.2' because it was <2 characters long Warning: skipping read 'SRR9878469.244378.1' because length (1) <= # seed mismatches (0)

The loss of these reads couldn't be ignored because it does not allow to reproduce the PairMapper correlations previously published.

Wondering if the conversion to SRA does change the quality of the reads?

Psirving commented 4 years ago

Hello, are you still having trouble replicating the published result? These warnings look to me like the expected and desired behavior of ShapeMapper2, and I would not expect them to change the final result. If you are getting an entirely different answer from what was published, please send me your log files and PairMapper output files and I'll try to figure out why.

afafbioinfo commented 4 years ago

Hello, Thank you, yes I m not able to reproduce the published results, I realized that I m using the version 2.1.5 please how can I get a the version 2.1.4 of SHAPEMapper? Thank you,

Le lun. 10 févr. 2020 à 14:14, Patrick Irving notifications@github.com a écrit :

Hello, are you still having trouble replicating the published result? These warnings look to me like the expected and desired behavior of ShapeMapper2, and I would not expect them to change the final result. If you are getting an entirely different answer from what was published, please send me your log files and PairMapper output files and I'll try to figure out why.

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Psirving commented 4 years ago

This link will download the 1.1 Gb tarball for version 2.1.4.

https://github.com/Weeks-UNC/shapemapper2/releases/download/2.1.4/shapemapper-2.1.4.tar.gz

afafbioinfo commented 4 years ago

I was able to reproduce the Pair-map correlation results using SHAPEMapper 2.1.4 with the original fastq. It seems that SRA formatting is kind of affecting the quality of the reads.
Thank you,