FLAMES

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minimap error using sc_long_pipeline.py

1

Hi @LuyiTian , Could you please comment on my error below? Running code: ``` for i in test; do /FLAMES/python/sc_long_pipeline.py --gff3 hg38v99.Cellranger.genes.gtf --infq $i.demultiplexed.fq.gz --outdir FLAMES_Output/$i --genomefa hg38v99.Cellranger.genome.fa --config_file /FLAMES/config_sclr_nanopore_default.json...

aheravi

Demultiplexing

12

Can this pipeline also demultiplex reads from cell barcodes?

callumparr

Demultiplexing issues

3

Hi Luyi, The pipeline is great! Thanks for the effort and for sharing it. I have tried FLAMES on your published data and our own in-house data, and have two...

yangao07

where is your whiltelist

1

In your script file, not find filtered_feature_bc_matrix/barcodes.tsv.gz

markme123

config file

3

Hi, Nice work! Congrats! Two questions: 1- Can I use the config file from the example ("SIRV_config.json") to run my human datasets? 2- Also, I could not activate the environment...

aheravi

Hi, Thank you for development of nice tool. I'm applying BLAZE and FLAMSE to my single cell ONT data. I've gotten useful output, but I need a genomic coordinate for...

hyeon9

Hello, Thanks for developing the tool. I was wandering if there is a way to get the gene name in the output matrix instead of the transcript_ID or the gene_ID...

rania-o

Hi, thanks for developing FLAMES, very nice tool. One question about the transcript_count.csv.gz output, I got the result like this:  Where the transcript id name is quite weird, do...

Qirongmao97

Hi, Thank you for this tool. I would like to know if we can only run mutation analysis without full-length transcriptome splicing. I have mapped bam and barcodes files. Thanks

choudharis2

Hi, I am getting this error in the final counts matrix generation step: does anyone know how to circumvent this issue? ``` b'[bam_sort_core] merging from 9 files and 12 in-memory...

sparthib