Open sparthib opened 1 week ago
You can copy / symlink the BAM files to the output folder, name them as [corresponding_fastq_file_name]_align2genome.bam
, e.g. if you have sample1.fastq
and sample2.fastq
, then put sample1_align2genome.bam
and sample2_align2genome.bam
should make FLAMES skip the alignment step and use the provided BAM.
This will also work for realignment (sample1_realign2transcript.bam
).
great thanks!
is there a similar multi-sample pipeline for bulk samples? Thanks!
Sowmya
For now, you could put all FASTQs into one folder and provide the path to the folder, each FASTQ file would be considered a sample and the [corresponding_fastq_file_name]_align2genome.bam
file could skip the alignment step.
The plan is to make this the same as the sc_long_multisample_pipeline in the devel branch where you could simply provide a named vector, where values could be path to folder or file:
sc_long_multisample_pipeline(
fastqs = c(
"sample1" = file.path(outdir, "fastq", "your_fq_folder_for_1st_sample"),
"sample2" = file.path(outdir, "fastq", "your_second_fq.fq.gz"),
"sample3" = file.path(outdir, "fastq", "third.fq.gz")),
...
)
And then the names would be used as sample names
Hi there,
I have generated BAM files for all my samples manually using minimap2, what would be the format to pass these onto
sc_long_multisample_pipeline
? I see options listed for passing the FASTQ files to the function in the documentation, is it similar for the bams?Thanks, Sowmya