I am trying to run this kallisto (latest) quant and all I get are abundance and json files.
kallisto quant --plaintext -t 4 -o rf-stranded.nob.1K1_L7.0 -i mm9_ref.idx --rf-stranded 1K1_L7.0 2K1_L7.0
the results files in stderr is:
[quant] fragment length distribution will be estimated from the data
[index] k-mer length: 15
[index] number of targets: 23
[index] number of k-mers: 363,704,628
[index] number of equivalence classes: 1,945,936
[quant] running in paired-end mode
[quant] will process pair 1: 1K1_L1.0
2K1_L1.0
[quant] finding pseudoalignments for the reads ... done
[quant] processed 22,897,424 reads, 4,476,549 reads pseudoaligned
[quant] estimated average fragment length: 24.2427
[ em] quantifying the abundances ... done
[ em] the Expectation-Maximization algorithm ran for 52 rounds
I get an abundance file with:
target_id length eff_length est_counts tpm
chr1 197195432 1.89745e+08 253015 21.3249
chr10 129993255 1.31621e+08 210320 25.5544
chr11 121843856 1.38776e+08 263606 30.3773
chr12 121257530 1.23195e+08 143568 18.6371
chr13 120284312 1.22484e+08 132969 17.3613
chr14 125194864 1.20926e+08 112711 14.9058
chr15 103494974 1.07866e+08 109335 16.2102
chr16 98319150 9.70075e+07 109045 17.9767
chr17 95272651 1.06375e+08 169166 25.4322
chr18 90772031 9.23542e+07 121990 21.1241
chr19 61342430 7.23377e+07 157142 34.7407
chr2 181748087 1.81791e+08 244870 21.5414
chr3 159599783 1.45978e+08 209257 22.9247
chr4 155630120 1.61978e+08 226893 22.4014
chr5 152537259 1.65672e+08 194951 18.8186
chr6 149517037 1.43243e+08 246652 27.5373
chr7 152524553 1.82795e+08 197527 17.2812
chr8 131738871 1.50556e+08 203954 21.6643
chr9 124076172 1.30446e+08 222639 27.295
chrX 166650296 1.40278e+08 176259 20.0942
chrY 15902555 5.76797e+07 123.462 0.0342311
mtDNA 16299 11804.8 737285 998819
rDNA 249368 720854 33272.5 738.159
run_info.json:
"n_targets": 23,
"n_bootstraps": 100,
"n_processed": 22897424,
"n_pseudoaligned": 4476549,
"n_unique": 3641646,
"p_pseudoaligned": 19.6,
"p_unique": 15.9,
"kallisto_version": "0.46.1",
"index_version": 10,
"start_time": "",
"call": "kallisto quant --plaintext -t 4 -b 100 -o rf-stranded.1K1_L1.0 -i mm9_ref.idx --bias --rf-stranded --gtf UCSC_genes.gtf --pseudobam --genomebam 1K1_L1.0.gz 2K1_L1.0.gz"
}
When I ran it with boot strapping (-b), -gtf and --pseudobam --genomebam it gave me a bam file.
44879990 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
8078785 + 0 mapped (18.00% : N/A)
44879990 + 0 paired in sequencing
22439995 + 0 read1
22439995 + 0 read2
8077160 + 0 properly paired (18.00% : N/A)
8077160 + 0 with itself and mate mapped
1625 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
I'm not sure what is going wrong, can someone help?
NOTE I use a 15nt kmer, and this about 1/2 of what is suggested (31 I think), is that a problem?
I probably should give a file of transcripts to the index step and not a chromosome fileNot probably, you must. Kallisto strictly pseudoaligns against a transcriptome, that is its mode of operation. $\endgroup$