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r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
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--barcode-file option from snaptools snap-pre doesnt seem to work #84

Closed opoirion closed 5 years ago

opoirion commented 5 years ago

Hi Rongxin.

the --barcode-file option from the snaptools seem to have no effect:

snaptools snap-pre --input-file tmp.repl1_TEST5.sorted.bed.gz --genome-size mm10.genome.size --output-snap repl1_TEST5.snap --barcode-file tmp.repl1_TEST5.xgi --overwrite True --genome-name mm10 --keep-chrm False

and

snaptools snap-pre --input-file tmp.repl1_TEST5.sorted.bed.gz --genome-size mm10.genome.size --output-snap repl1_TEST5.snap --overwrite True --genome-name mm10 --keep-chrm False

give both a snap file with the same number of barcodes (equal to the total number of barcodes in the dataset)

r3fang commented 5 years ago

Hi Olivier,

Indeed, it is a problem that I have fixed for a while. This problem is caused by the conflict between —min-cov and —barcode-file. But it should be fixed now. If you can update to the latest version 1.4.8, the problem should be gone.

Best,

Rongxin Fang, Ren Lab Ludwig Cancer Research Bioinformatics Ph.D. Student University of California, San Diego

On Sep 4, 2019, at 3:43 PM, Poirion olivier notifications@github.com wrote:

Hi Rongxin.

the --barcode-file option from the snaptools seem to have no effect:

snaptools snap-pre --input-file tmp.repl1_TEST5.sorted.bed.gz --genome-size mm10.genome.size --output-snap repl1_TEST5.snap --barcode-file tmp.repl1_TEST5.xgi --overwrite True --genome-name mm10 --keep-chrm False

and

snaptools snap-pre --input-file tmp.repl1_TEST5.sorted.bed.gz --genome-size mm10.genome.size --output-snap repl1_TEST5.snap --overwrite True --genome-name mm10 --keep-chrm False

give both a snap file with the same number of barcodes (equal to the total number of barcodes in the dataset)

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