Examples

HTSinfer provides easy-to-use commands for analyzing single- and paired-ended RNA-Seq libraries.

Single-ended library example

To run HTSinfer on a single-ended RNA-Seq library, use the following command:

htsinfer tests/files/adapter_single.fastq

Paired-ended library example

To run HTSinfer on a paired-ended RNA-Seq library, use the following command:

htsinfer tests/files/adapter_1.fastq tests/files/adapter_2.fastq

Both commands will output the results in JSON format to STDOUT and the log to STDERR.

Example output

Here is a sample output for the paired-ended library:

{
   "library_stats": {
      "file_1": {
         "read_length": {
            "min": 75,
            "max": 75,
            "mean": 75.0,
            "median": 75,
            "mode": 75
         }
      },
      "file_2": {
         "read_length": {
            "min": 75,
            "max": 75,
            "mean": 75.0,
            "median": 75,
            "mode": 75
         }
      }
   },
   "library_source": {
      "file_1": {
         "short_name": "hsapiens",
         "taxon_id": "9606"
      },
      "file_2": {
         "short_name": "hsapiens",
         "taxon_id": "9606"
      }
   },
   "library_type": {
      "file_1": "first_mate",
      "file_2": "second_mate",
      "relationship": "split_mates"
   },
   "read_orientation": {
      "file_1": "SF",
      "file_2": "SR",
      "relationship": "ISF"
   },
   "read_layout": {
      "file_1": {
         "adapt_3": "AATGATACGGCGACC",
         "polyA_frac": 10.0
      },
      "file_2": {
         "adapt_3": "AATGATACGGCGACC",
         "polyA_frac": 10.0
      }
   }
}

Results

• library_stats: Read length statistics results, including the minimum, maximum, mean, median and mode.

• library_source: Library source inference results, with the short name and NCBI taxonomy ID of the source organism.

• library_type: Library type inference results, single- or paired-end. In case of paired-end samples, the mate designation.

• read_orientation: Read orientation inference results, based on the fragment library types notation from Salmon.

• read_layout: Read layout inference results, including the 3’-adapter sequence and the poly(A) fraction.

For more details on the output structure, refer to the Results model in the API documentation.