search

akdess / CaSpER

76 stars 27 forks source link

Creating loh object from BAFExtract output #4

Closed joeymays closed 4 years ago

joeymays commented 5 years ago

Hi,

I have a question concerning the expected output for BAFExtract. I'm running the following line in R after running the BAFExtract code below:

loh <- readBAFExtractOutput ( path=."/placenta_BAF_output", sequencing.type="single-cell")

samtools view ./cellranger3/outs/*.bam | ../BAFExtract -generate_compressed_pileup_per_SAM stdin ./GRCh38.list ./placenta_BAF_output/ 50 0

../BAFExtract -get_SNVs_per_pileup ./GRCh38.list ./placenta_BAF_output/ ./BAFExtract_genome/ 20 4 0.1 ./placenta_6220.baf

I'm getting a "cannot open file" error from the R function; it seems to be expecting files in the output directory with a .snp tag in the filename. Should there be other files output from the -get_SNVs_per_pileup in addition to the .baf file?

olferievm commented 5 years ago

It is not working for me. I generated output files with BAFExtract based on the example provided. There are no .snp type files. The command below can't work as there is no such type of files. Could you explain from were .snp files should be obtained?

loh <- readBAFExtractOutput ( path="./meningioma_baf\", sequencing.type="bulk") Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file './meningioma_baf\/NA': No such file or directory

peter-yufan-zeng commented 4 years ago

I am running into the same issues as mentioned above. @akdess any way to fix this issue? Thanks in advance!

akdess commented 4 years ago

@peter-yufan-zeng @olferievm @joeymays I am very sorry for my late reply. I have updated the readBAFExtractOutput function, you should specify the BAFExtract file extension as a parameter. If the output of BAFExtract is .baf files then you should say readBAFExtractOutput ( path="./meningioma_baf\", sequencing.type="bulk", suffix="baf") Hope it helps.