counts are not gene

[sdwien]

The quant.sf files that are generated by sample (pipeline-transcriptome-de_phe/counts/$samplename_salmon), when I run the pipeline, look like this (mouse genome):

Name    Length  EffectiveLength TPM     NumReads
chr1    195471971       195471722.000   37832.318871    94666.189
chr2    182113224       182112975.000   44177.212938    102988.135
chr3    160039680       160039431.000   56700.439152    116161.287
chr4    156508116       156507867.000   62252.200494    124720.796
chr5    151834684       151834435.000   21599.692789    41982.263
chr6    149736546       149736297.000   28423.282601    54481.532
chr7    145441459       145441210.000   93232.389098    173581.039
chr8    129401213       129400964.000   53266.152592    88234.176
chr9    124595110       124594861.000   28806.345603    45944.792
chr10   130694993       130694744.000   109556.806254   183292.831
chr11   122082543       122082294.000   86232.333615    134763.044
chr12   120129022       120128773.000   51734.803277    79556.897
chr13   120421639       120421390.000   30402.046775    46865.629
chr14   124902244       124901995.000   9604.455594     15356.425
chr15   104043685       104043436.000   90960.906485    121148.337
chr16   98207768        98207519.000    17191.145805    21612.129
chr17   94987271        94987022.000    28660.455170    34849.403
chr18   90702639        90702390.000    38024.378414    44149.811
chr19   61431566        61431317.000    99570.377773    78301.120
chrX    171031299       171031050.000   11767.443247    25763.512
chrY    91744698        91744449.000    4.813453        5.653

Isn't it supposed to hold the counts for each transcript in the annotated genome?
As a consequence, other errors come up in the steps run in R for DE.
Any help or suggestion is very much appreciated.
Best, Sophia

[bsipos]

Well, it looks like you used the genome reference instead of the mouse transcriptome reference! Switch to the correct transcriptome reference and the problem will be solved.