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bcgsc / RNA-Bloom

:hibiscus: reference-free transcriptome assembly for short and long reads
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Sequence header #14

Closed giantoni closed 3 years ago

giantoni commented 3 years ago

Hi,

I am so sorry for this question, but I didn't find an explanation of the sequence header of RNA-Bloom output.

All my sequences have this type of header: >E4.L.4 l=306. Please, confirm if I am right:

E4 is the gene number and L4 is the isoform number?

Many thanks in advance!

Gi

rnabloom -left sample_1_R1.fastq.gz -right sample_1_R2.fastq.gz -revcomp-right -ntcard -t 80 -outdir sample1_transcriptome

kmnip commented 3 years ago

Hi,

There is currently no gene name assigned in RNA-Bloom. E4.L.4 is the isoform name. E4 indicates that the isoform was extended from a fragment with minimum k-mer coverage >= 10,000 (1E4). L indicates that the seed fragment was longer than the minimum fragment length threshold.

Ka Ming

Akanksha2511 commented 2 years ago

Hi, can you please explain the sequence header. For example in here ">2 l=3215 c=1529.4984 s=2" what is the before and after . part of c.

Thanks, Akanksha

kmnip commented 2 years ago

l is the sequence length s is the ID of the seed sequence to used from the previous stage

Akanksha2511 commented 2 years ago

Could you please also explain what is c in the sequence header.

Thanks, Akanksha

On Thu, 10 Feb 2022 at 7:23 pm, Ka Ming Nip @.***> wrote:

l is the sequence length s is the ID of the seed sequence to used from the previous stage

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kmnip commented 2 years ago

c is the estimated per-base read depth. It's very experimental, not very accurate.