Understanding minimap2 output (PAF format)
0
0
Entering edit mode
12 months ago

Hi all! I used minimap2 in order to align a (subset) of transcripts from an older project to the set of transcripts I generated to my project. The command I used was the following:

minimap2 my_transcriptome.fasta --secondary=no oldproject_transcripts.fasta > minimap_output.txt

As is my understanding, minimap flags the highest-scoring alignment as the primary. However, after analyzing my output, I´m pretty sure my rationale is wrong, as I got several primary alignments reported to the same query. Can someone explain why this happens? Thanks in advance

partial output:

Caros006251.1_4 5238    1052    3241    -   CATHA.6748.1    2205    14  2201    1446    2198    60  tp:A:P  cm:i:212    s1:i:1444   s2:i:471    dv:f:0.0445 rl:i:18
Caros006251.1_4 5238    8   812 +   CATHA.11089.1   3445    1248    2052    683 804 6   tp:A:P  cm:i:119    s1:i:683    s2:i:666    dv:f:0.0193 rl:i:18
minimap2 PAF Parsing RNA-SEQ • 1.1k views
ADD COMMENT

Login before adding your answer.

Traffic: 1651 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6