alevin library type for 10x Chromium v3

[deevdevil88]

Hi,
i just wanted confirm if the library type for alevin quant for 10x chromium 3' v3 is still ISR?

Best,
Devika

[k3yavi]

Yep, that's correct.

[lianos]

Is there maybe a mistake in the "improving-txome-specificity" alevin-fry tutorial, then?

The current command library type specified to align the pbmc_10k_v3 reads is -l IU instead of -l ISR:

salmon alevin -i grch38_splici_idx -p 16 -l IU --chromiumV3 --sketch \
-1 pbmc_10k_v3_fastqs/pbmc_10k_v3_S1_L001_R1_001.fastq.gz \
pbmc_10k_v3_fastqs/pbmc_10k_v3_S1_L002_R1_001.fastq.gz \
-2 pbmc_10k_v3_fastqs/pbmc_10k_v3_S1_L001_R2_001.fastq.gz \
pbmc_10k_v3_fastqs/pbmc_10k_v3_S1_L002_R2_001.fastq.gz \
-o pbmc_10k_v3_map \
--tgMap t2g.tsv

[rob-p]

Thanks for the feedback @lianos. The reason thats not a typo is that in the alevin-fry pipeline, unlike alevin, the filtering is done in the "generate permit list" and collate steps. Thus, when you specify -d fw in the generate-permit-list command you are telling alevin-fry to keep only those mappings in the forward orientation. Alevin doesn't have an independent filtering command, so it must all be enforced via the library type.

[lianos]

Ohh ... I see, thanks for the explanation!