FLAMES

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On [line 88](https://github.com/LuyiTian/FLAMES/blob/18fb83c7f09baf8325efac1506ef5380de580661/python/count_tr.py#L88), read_dict[r][0] will be assigned with `(tr, rec.get_tag("AS"), tr_cov, float(rec.query_alignment_length)/rec.infer_read_length(), rec.mapping_quality)`, contradicting the comment on [line 106](https://github.com/LuyiTian/FLAMES/blob/18fb83c7f09baf8325efac1506ef5380de580661/python/count_tr.py#L106) `# transcript_id, pct_ref, pct_reads`. `hit[1] > 0.8` was used on [line...

ChangqingW

Ciao Luyi Thanks again for nice work, could you please let me know what's the difference between FSM (which is based on the definition of SQANTI isoformas matched with reference...

parsboy66

Hello, I was trying to use FLAMES in a isoform characterization benchmarking study with a single sample but, since I am new with the long-read world, it is not clear...

apc1992

run match_cell_barcode, no error, no result, match_cell_barcode /data_RAGE_seq/data1 cell_barcode_stat.txt split_barcode.fastq flame_3M-february-2018.txt 2; split_barcode.fastq is zero,no other file generation。

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markme123

Config file parameters

1

Hi, I am currently using FLAMES and a few other assemblers (flair and bookend), to compare them against each other and find out, which would be the most optimal one...

hacaoe

Using transcript_count.csv.gz matrix with popular analysis tools

1

I'm struggling to convert transcript_count.csv.gz matrix to a Seurat or AnnData object? Any help and advice would be appreciated.

rakszewska

What's the difference

1

hi ~ What's the difference between `barcode hm match` and `barcode match`.

haowBio

match_cell_barcode qnames too long

2

Minimap2/Samtools is throwing an error from reads with append cell barcode/UMI (generated from `match_cell_barcode`). ``` [E::sam_parse1] query name too long [W::sam_read1_sam] Parse error at line 8760987 samtools sort: truncated file....

danledinh

Compute resource allocation?

2

Is there a way to define number of cores, RAM usage, etc. for the pipelines?

danledinh

hi~ I remember that you use FLAMES to detect mutation and plot the mutation in UMAP. I was so impressed by this part. However I notice that "mutation detection" was...

garfield-hu