snap has no AM session

[hjack123]

$ snaptools snap-pre \ --input-file=atac_v1_adult_brain_fresh_5k.snap.nsrt.bam \ --output-snap=atac_v1_adult_brain_fresh_5k.snap \ --genome-name=mm10 \ --genome-size=mm10.chrom.sizes \ --min-mapq=30 \ --min-flen=50 \ --max-flen=1000 \ --keep-chrm=TRUE \ --keep-single=FALSE \ --keep-secondary=False \ --overwrite=True \ --max-num=20000 \ --min-cov=500 \ --verbose=True

I created snap with 10x outputs bam file. but then

showBinSizes(snapfile); [1] "Warning @check.bin.size: '/AM/binSizeList' not found in test.snap" numeric(0) x.sp = addBmatToSnap(x.sp, bin.size=5000, num.cores=1); [1] "error: the following nsap files do not contain AM session"

How do i write the AM session? Thank you!!

[yeswzc]

Hi Hjack123, Could you tell me how did you solve this issue? (if you did)

Thanks! ZC

[r3fang]

Hi,

You need to run add-bmat after running snap-pre

Sent from my iPhone

On Sep 28, 2019, at 11:20 PM, Zhichao Wu notifications@github.com wrote:

Hi Hjack123, Could you tell me how did you solve this issue? (if you did)

Thanks! ZC

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[yeswzc]

Hi, You need to run add-bmat after running snap-pre … Sent from my iPhone On Sep 28, 2019, at 11:20 PM, Zhichao Wu @.***> wrote: Hi Hjack123, Could you tell me how did you solve this issue? (if you did) Thanks! ZC — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

Thanks for your amazing quick reply.

[brianpenghe]

Hi Hjack123, Could you tell me how did you solve this issue? (if you did)

Thanks! ZC

snaptools snap-add-bmat \
    --snap-file=possorted_bam.snap \
    --bin-size-list 1000 5000 10000 \
    --verbose=True