Unclear output doc figure for Samtools flagstat and add MALT/KRAKEN/MVA etc.

[jfy133]

Aida pointed out that the image by @ZandraFagernas for Samtools flagstat might be misleading.

Equal sequencing depth makes sense for screening or initial runs, but is not what would be needed for deep sequencing projects.

Secondly, mapped reads being equal of course would be amazing but rarely encountered in real life.

We should consider making a caveat (e.g. asterisk saying that we are assuming the above, or when no a priori knowledge of endogenous NDA content), or add extra panels.

[jfy133]

@ZandraFagernas

Can you do the following:

• Flip pannel A and C
• Rephase 'new' panel A as: In an ideal world of equal sequencing pooling and equal endogenous DNA
• Rephrase 'new' panel C: This can be OK when unequal number of reads were requested per sample but equal endogenous DNA.
• Rephrase panel B: This is standard for initial preservation screening of aDNA with equal sequencing pooling and variable endogenous DNA.

[jfy133]

Reference:

and you can rephrase to condense ifneeded

[jfy133]

@ZandraFagernas Also the following needs to be updatd:

Whereby poop1_lane4_SE needs to merge with the other PE lanes (i.e. same time as the library above); this behaviour will be changing in an upcoming PR (#503) because it was too restrictive.

[jfy133]

@ZandraFagernas the same issue in the Samtools image above also is for 'FASTQC - Sequence Count' panel A regarding the uneeven sequencing. Could you tweak the phrasing make clear this is for initial screening

[apeltzer]

Is this fixed now?

[jfy133]

Yes!