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snijderlab
Template-based assembly of proteomics short reads for de novo antibody sequencing and repertoire profiling
When I use Stitch to read the [results.zip](https://github.com/snijderlab/stitch/files/13682437/results.zip) of pNovo v3.1.5 and run [new_PNovo_FLAG_H_20ppm_ALC90.txt](https://github.com/snijderlab/stitch/files/13682439/new_PNovo_FLAG_H_20ppm_ALC90.txt)an error occurs:， It seems that Stitch encountered an issue in recognizing the length of the sequence...
Allowing users to read in MaxQuant database searches would allow some nice analyses we normally do on de novo data to be done on database data with a bit more...
Here is a very nice example where a couple of problems are visible: * Too short overhang for the last two reads * Slightly misaligned reads, asking the question if...
Per read it is known which protease generated the peptide, this can be used in the assignment of hard amino acids. Chymotrypsin is known to have specificity after I/L. But...
If common errors occur in the consensus alignment (D/N. Q/E-pyro) it could be nice to highlight them and give an explanation for why this mistake could be made on the...
It has occurred a couple of times that multiple peptides with the same precursor mass where placed close to each other, with only one of the peptides actually having a...
Allow the user to specify that on low DOC positions the germline should be taken instead of the consensus sequence. This could also be a more gray definition where the...
 As can be seen above, the gap in the cdr2 breaks the annotation in this graph, and this one only. (The consensus logo and reads alignment are correct.)
So one for FR1, CDR1, FR2, etc. The hope is that running it in this way would result in less 'split' reads. Because now if the program is ran with...
In GitLab by @nonnominandus on Jul 16, 2021, 17:37 It would be great if all found PTMs plus possible ones could be annotated in the result HTML. Of course this...
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Template-based assembly of proteomics short reads for de novo antibody sequencing and repertoire profiling