Issues with building an index in salmon

Question

[oma219]

Hello,

I was building an index with Salmon and had some of these warnings come up with the index was being built. Are these warnings usually indications that the wrong file was used to make the index? Thanks.

/home/ubuntu/software/Salmon-0.8.2_linux_x86_64/bin/salmon index -t /home/ubuntu/data/rnaseq/nematostella/venus/genome/Nematostella_vectensis.GCA_000209225.1.dna.toplevel.fa          -i nematostella_index


iptome and not a genome?
[2017-06-04 08:24:14.775] [jointLog] [warning] Entry with header [NEMVEscaffold_369] was longer than 200000 nucleotides.  Are you certain that we are indexing a transcriptome and not a genome?
[2017-06-04 08:24:14.785] [jointLog] [warning] Entry with header [NEMVEscaffold_377] was longer than 200000 nucleotides.  Are you certain that we are indexing a transcriptome and not a genome?
[2017-06-04 08:24:14.795] [jointLog] [warning] Entry with header [NEMVEscaffold_374] was longer than 200000 nucleotides.  Are you certain that we are indexing a transcr

[WouterDeCoster]

I would suggest paying more attention at the manual, which states:

If you want to use Salmon in quasi-mapping-based mode, then you first have to build an Salmon index for your transcriptome. Assume that transcripts.fa contains the set of transcripts you wish to quantify. First, you run the Salmon indexer:

./bin/salmon index -t transcripts.fa -i transcripts_index --type quasi -k 31

The warnings you get are VERY descriptive of what is wrong.

[WouterDeCoster]

Hi oma219,

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

Cheers, Wouter

Answer 1

[andrew.j.skelton73]

You're trying to create a Salmon transcriptome index from the top-level genome sequence. You need a fasta file with all the individual transcript sequences to build the index. The warning is suggestive of this.