![]() (nanocount) transcript_name raw est_count tpm Progress: 2.00 rounds Įxit EM loop after 2 rounds Convergence value: 0.0019361726963877538 # Summarize data # Convert results to dataframe Compute estimated counts and TPM Write file # Checking options and input files # Initialise Nanocount # Parse Bam file and filter low quality alignments Summary of alignments parsed in input bam file Valid alignments: 150,517 Discarded unmapped alignments: 9,545 Discarded alignment with invalid 3 prime end: 6,133 Discarded negative strand alignments: 4,515 Discarded supplementary alignments: 334 Summary of reads filtered Reads with valid best alignment: 85,908 Invalid secondary alignments: 60,120 Valid secondary alignments: 2,622 Reads with low query fraction aligned: 1,628 Generate initial read/transcript compatibility index # Start EM abundance estimate # q, -quiet Reduce verbosity (default: False) v, -verbose Increase verbosity for QC and debugging (default: In conjunction with max_dist_3_prime itĬan be used to select near full transcript reads only Maximum distance of alignment start to 5 prime of u MAX_DIST_5_PRIME, -max_dist_5_prime MAX_DIST_5_PRIME In ONT dRNA-Seq reads are assumed to startįrom the polyA tail (-1 to deactivate) (default: 50) Maximum distance of alignment end to 3 prime of d MAX_DIST_3_PRIME, -max_dist_3_prime MAX_DIST_3_PRIME Retain any supplementary alignments and considered choices = (default: Use either the primary alignment defined by theĪligner ("primary") or the longest alignment Score (AS optional field), but it can be changed to Byĭefault ("alignment_score") uses the best alignment Method to pick the best alignment for each read. p PRIMARY_SCORE, -primary_score PRIMARY_SCORE To the output file (required valid bam/sam header) x, -extra_tx_info Add transcripts length and zero coverage transcripts Maximum number of EM rounds before triggering stop e MAX_EM_ROUNDS, -max_em_rounds MAX_EM_ROUNDS c CONVERGENCE_TARGET, -convergence_target CONVERGENCE_TARGETĬonvergence target value of the cummulative differenceīetween abundance values of successive EM round to Length of secondary alignments compared to the primaryĪlignment to be considered valid alignments (default: t SEC_SCORING_THRESHOLD, -sec_scoring_threshold SEC_SCORING_THRESHOLDįraction of the alignment score or the alignment "alignment_length" (default: alignment_score) Value to use for score thresholding of secondary s SEC_SCORING_VALUE, -sec_scoring_value SEC_SCORING_VALUE Minimal fraction of the primary alignment queryĪligned to consider the read valid (default: 0.5) f MIN_QUERY_FRACTION_ALIGNED, -min_query_fraction_aligned MIN_QUERY_FRACTION_ALIGNED Minimal length of the alignment to be considered valid l MIN_ALIGNMENT_LENGTH, -min_alignment_length MIN_ALIGNMENT_LENGTH Reads selected by NanoCount to perform quantificationĮstimation (BAM format) (default: None) Optional output file path where to write filtered b FILTER_BAM_OUT, -filter_bam_out FILTER_BAM_OUT Output file path where to write estimated counts (TSV ONT dRNA-Seq reads including secondary alignments Sorted and indexed BAM or SAM file containing aligned i ALIGNMENT_FILE, -alignment_file ALIGNMENT_FILE version show program's version number and exit ![]() h, -help show this help message and exit Kallisto, salmon, etc to handle the uncertainty of multi-mapping reads Sequencing* datasets, using an expectation-maximization approach like RSEM, ![]() NanoCount estimates transcripts abundance from Oxford Nanopore *direct-RNA
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