Invalid alphabet

[barkait]

Hey,

When i am parsing my data (which is kind of artificial) there is some entries that are classified as "invalid alphabet". Meanwhile i can't share my FASTQ files, but you might elaborate what is exactly "invalid alphabet"?

Best,

[drivenbyentropy]

Hi,

Invalid Alphabet means that the read was discarded because it contained a letter which did not correspond to A C G or T. In FastQ files this typically corresponds to occurrences of N.

If your data is artificial and you know for sure no invalid nucleotides occur, there might be a bug in the parser which is assigning the read to this case by mistake.

If you can provide me with a minimal example where you encounter this issue, I will be more than happy to look into it.

Thank you for reporting this!

[PJpb]

I can’t log in right now to github but i’ve had the same issue. For me it was due to the files not being UNIX and UTF-8 coded. Might be the same thing?

W dniu pt., 30.03.2018 o 09:16 drivenbyentropy notifications@github.com napisał(a):

Hi,

Invalid Alphabet means that the read was discarded because it contained a letter which did not correspond to A C G or T. In FastQ files this typically corresponds to occurrences of N.

If your data is artificial and you know for sure no invalid nucleotides occur, there might be a bug in the parser which is assigning the read to this case by mistake.

If you can provide me with a minimal example where you encounter this issue, I will be more than happy to look into it.

Thank you for reporting this!

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[barkait]

as you said, i found some N's in my data, so that must be the reason. thanks!

[drivenbyentropy]

I have add a description regarding the meaning of the individual parsing statistics to the Wiki.

Thanks again!