Question: How can I produce gene level quantification using Salmon pseudo-aligner?
0
gravatar for Angelique
17 months ago by
Angelique10
Angelique10 wrote:

Hi !

I am using Salmon in order to permform pseudo-alignment on paired end rna-seq data. I want a gene quantification but i obtain files cith transcripts quantification : command line used : salmon quant -i Transcriptome_GH38_release_92/Homo_sapiens.GRCh38.92.cdna.ncrna.fa_quasi_index/ -l A -1 Test/SRX2264036_1.fastq.gz -2 Test/SRX2264036_2.fastq.gz -o test_quanti_36 -p 8

extract of obtained quantification file :

Name Length EffectiveLength TPM NumReads ENST00000434970.2 9 5.093 0.000000 0.000000 ENST00000448914.1 13 6.885 0.000000 0.000000 ENST00000415118.1 8 4.489 0.000000 0.000000 ENST00000632684.1 12 6.443 0.000000 0.000000 ENST00000430425.1 17 9.050 0.000000 0.000000 ENST00000390578.1 31 15.313 0.000000 0.000000 ENST00000450276.1 17 9.050 0.000000 0.000000 ENST00000431870.1 16 8.504 0.000000 0.000000 ENST00000390567.1 20 10.664 0.000000 0.000000 ENST00000390590.1 31 15.313 0.000000 0.000000

I tried to used the -g option to provide a gtf annotation file but the resulting file is still at the transcript level.

How can I produce gene level quantification using Salmon ?

Thank you & Have a good day

ADD COMMENTlink modified 17 months ago by stefanos.bamopoulos30 • written 17 months ago by Angelique10
2
gravatar for ATpoint
17 months ago by
ATpoint26k
Germany
ATpoint26k wrote:

Never used Salmon with -g but there is the tximport package to aggregate transcript quantifications to the gene level. Was developped for exactly this purpose.

ADD COMMENTlink modified 17 months ago • written 17 months ago by ATpoint26k
0
gravatar for stefanos.bamopoulos
17 months ago by
stefanos.bamopoulos30 wrote:

It is also possible to get counts aggregated on the gene level with salmon directly. I am not aware of the exact command on the command line, since I run salmon on the Galaxy platform, but it is possible to provide a table matching each transcript to a gene and get a seperate output for counts at the transcript and the gene level.

Note that depending on which tool you will use for your downstream analysis you will need either TPM or raw counts.

ADD COMMENTlink written 17 months ago by stefanos.bamopoulos30
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