Kristoffer
Kristoffer
So as for the `MISMATCH_MATE_CIGAR_STRING` I believe this is simply the `=/X` cigars conversion to `M` - so no problem there (unless some caller gets hung up on this warning)....
Ah, I see. This is also an error caused by the program adding the attributes to the bam file. For some reason, picard does not like that the cigar of...
Thanks for your help @mohsenzakeri; it is appreciated. The way I interpret this is to do this: ``` $ export PATH="/proj/snic2020-15-201/anaconda3/envs/cmake/include:$PATH" $ export PATH="/proj/snic2020-15-201/anaconda3/envs/cmake/lib:$PATH" $ cmake -DCMAKE_C_COMPILER=/proj/snic2020-15-201/anaconda3/envs/cmake/bin/gcc -DCMAKE_CXX_COMPILER=/proj/snic2020-15-201/anaconda3/envs/cmake/bin/g++ ../ ```...
Hi @rob-p , Thanks, I can confirm that rebooting, removing complete pufferfish directory, and following the below steps got me a lot further. ``` $ git clone [email protected]:COMBINE-lab/pufferfish.git $ cd...
Spontaneous thoughts: 1. From your example it looks like `-N n` outputs `n - 1` extra alignments :) 2. the decrease in quality is probably because we do not consider...
Perhaps an obvious statement, but this issue made me think of a straightforward analysis for sanity check of the MAPQ outputs, as discussed in #25 and #52. If strobealign is...
Agreed with your last comment. The initial allocation of the flat_vector is based on a prediction of the number of seeds that will be created from the reference. The prediction...
It depends on what your input data is and what is the desired output of the analysis. Are all the reads within one file but with sample-specific barcods? maybe then...
Not sure it is possible to create an OTU table without some scripting. One idea: 1. Label all your reads in the headers (sample 1 gets a `_1` appended, etc)...