Comments about the pipeline

[MikiSchikora]

Good evening,

I'm Miquel Àngel Schikora, a MSc student of Lucas Carey's lab in the UPF of Barcelona. I have some questions about the pipeline I'd like to comment.

• Do you think that I can run your code in mac? It didn't work so far and I think it must be because a linux vs mac shell interpreting problem, as the makefile can't be executed, so that I thought it may be impossible to compile on mac. I successfully installed the pipeline on a linux machine.

• The code provided for converting a fastq to fasta gave an error to me. Instead I ran it like this: "awk 'BEGIN{P=1}{if(P==1||P==2){gsub("@",">");print $1}; if(P==4)P=0; P++;};' BASE_NAME
  -DCS.fastq > BASE_NAME-DCS.fasta". Do you think that it is correct?

• I couldn't run blat on the data and ran blast, with the tabular format (id 6). Do you think this is equivalent, so that anything else in the pipeline would be affected by this?

• I ran blast using the generated BASE_NAME-DCS.fasta. Is this correct?

• BASE_NAME-DCS.fastq has much more sequences (18517664 lines) than BASE_NAME-DEBREAKED.fastq (around 400000 lines). Is this expected?

• I got stuck at step 5 of the pipeline, and perhaps it is because I couldn't generate correctly the exonsWithFake.gff file. Could you provide me the file used originally as exonsWithFake.gff. I'm running refineBreakpoint-withIndels and getting an output like this: "terminate called after throwing an instance of 'std::out_of_range'" "what(): basic_string::substr". Which I can't interpret. Any idea?

• Overall it would be useful if you could provide some kind of processed dataset already available. Thanks

Thanks a lot for your time,

Miquel Àngel Schikora