Identical insert size and SD
Opened this issue · 0 comments
jamespblloyd-uwa commented
Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?
salmon (bulk mode)
Describe the bug
I did a lot of independent RNAseq libs recently and all came out with the identical frag_length mean and sd (see below). This surprised me greatly as while the libraries looked consistent on a tapestation, I would not expect them to be this consistent down to >7 decimal places. Also it is unclear how I can access fld.gz to see the raw data. MultiQC only shows me one distribution (for
frag_length_mean: 250.0000097391447
frag_length_sd: 25.001769513739427
Sample: Gam_0h_rep2A_RL5383_quant
frag_length_mean: 250.0000097391447
frag_length_sd: 25.001769513739427
Sample: Gam_0h_rep3A_RL5403_quant
frag_length_mean: 250.0000097391447
frag_length_sd: 25.001769513739427
Sample: Gam_3h_37C_rep1_RL5385_quant
frag_length_mean: 250.0000097391447
frag_length_sd: 25.001769513739427
Sample: Gam_3h_37C_rep2_RL5386_quant
frag_length_mean: 250.0000097391447
frag_length_sd: 25.001769513739427
Sample: Gam_3h_37C_rep3_RL5406_quant
frag_length_mean: 250.0000097391447
frag_length_sd: 25.001769513739427
Sample: Gam_3h_4C_rep1_RL5387_quant
frag_length_mean: 250.0000097391447
frag_length_sd: 25.001769513739427
Sample: Gam_3h_4C_rep2_RL5388_quant
frag_length_mean: 250.0000097391447
frag_length_sd: 25.001769513739427
Sample: Gam_3h_4C_rep3_RL5407_quant
frag_length_mean: 250.0000097391447
frag_length_sd: 25.001769513739427
Sample: Gam_3h_RT_rep1_RL5384_quant
frag_length_mean: 250.0000097391447
frag_length_sd: 25.001769513739427
Sample: Gam_3h_RT_rep2_RL5404_quant
frag_length_mean: 250.0000097391447
frag_length_sd: 25.001769513739427
Sample: Gam_3h_RT_rep3_RL5405_quant
frag_length_mean: 250.0000097391447
frag_length_sd: 25.001769513739427
Sample: Gam_6h_37C_rep1_RL5390_quant
frag_length_mean: 250.0000097391447
frag_length_sd: 25.001769513739427
Sample: Gam_6h_37C_rep2_RL5391_quant
frag_length_mean: 250.0000097391447
frag_length_sd: 25.001769513739427
Sample: Gam_6h_37C_rep3_RL5410_quant
frag_length_mean: 250.0000097391447
frag_length_sd: 25.001769513739427
Sample: Gam_6h_4C_rep1_RL5392_quant
frag_length_mean: 250.0000097391447
frag_length_sd: 25.001769513739427
Sample: Gam_6h_4C_rep2_RL5393_quant
frag_length_mean: 250.0000097391447
frag_length_sd: 25.001769513739427
Sample: Gam_6h_4C_rep3_RL5411_quant
frag_length_mean: 250.0000097391447
frag_length_sd: 25.001769513739427
Sample: Gam_6h_RT_rep1_RL5389_quant
frag_length_mean: 250.0000097391447
frag_length_sd: 25.001769513739427
Sample: Gam_6h_RT_rep2_RL5408_quant
frag_length_mean: 250.0000097391447
frag_length_sd: 25.001769513739427
Sample: Gam_6h_RT_rep3_RL5409_quant
frag_length_mean: 250.0000097391447
frag_length_sd: 25.001769513739427```
**To Reproduce**
Steps and data to reproduce the behavior:
Specifically, please provide at least the following information:
* Which version of salmon was used?
v1.10.0
* How was salmon installed (compiled, downloaded executable, through bioconda)?
Binary
* Which reference (e.g. transcriptome) was used?
Moss (Physco) v6.1 that I had generated
* Which read files were used?
* Which which program options were used?
`-l A -p 16 --validateMappings --numBootstraps 100 --seqBias --gcBias`
**Expected behavior**
A clear and concise description of what you expected to happen.
**Desktop (please complete the following information):**
- OS: Linux server: Rocky Linux release 8.5 (Green Obsidian)
- Version Rocky Linux release 8.5 (Green Obsidian)