text: user10409: 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?
  
  user77: As you surmised, kallisto requires a transcriptome fasta file, not a genome fasta file.
  
original_text: 10409: <p>I am trying to run this kallisto (latest) quant and all I get are abundance and json files.</p>
  <pre><code>kallisto quant --plaintext -t 4  -o rf-stranded.nob.1K1_L7.0 -i mm9_ref.idx  --rf-stranded 1K1_L7.0 2K1_L7.0
  </code></pre>
  <p>the results files in stderr is:</p>
  <pre><code>[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
  </code></pre>
  <hr />
  <p>I get an abundance file with:</p>
  <pre><code>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
  </code></pre>
  <p>run_info.json:</p>
  <pre><code>        &quot;n_targets&quot;: 23,
          &quot;n_bootstraps&quot;: 100,
          &quot;n_processed&quot;: 22897424,
          &quot;n_pseudoaligned&quot;: 4476549,
          &quot;n_unique&quot;: 3641646,
          &quot;p_pseudoaligned&quot;: 19.6,
          &quot;p_unique&quot;: 15.9,
          &quot;kallisto_version&quot;: &quot;0.46.1&quot;,
          &quot;index_version&quot;: 10,
          &quot;start_time&quot;: &quot;&quot;,
          &quot;call&quot;: &quot;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&quot;
  }
  </code></pre>
  <hr />
  <p>When I ran it with boot strapping (-b), -gtf and --pseudobam --genomebam it gave me a bam  file.</p>
  <pre><code>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&gt;=5)
  </code></pre>
  <p>I'm not sure what is going wrong, can someone help?</p>
  <p>NOTE I use a 15nt kmer, and this about 1/2 of what is suggested (31 I think), is that a problem?</p>
   77: <p>As you surmised, kallisto requires a transcriptome fasta file, not a genome fasta file.</p>
  