Hi there,
I encountered a confusing mapping issue with minimap2 when aligning a HiFi read from a tandem repeat region of Arabidopsis thaliana chromosome 1 (Chr1):
-
When aligning to the complete genome reference (all chromosomes): the read maps to Chr1 correctly with normal/negligible soft-clipping.
-
When aligning to the Chr1-only reference (extracted from the complete genome): the same read shows an unusually long soft-clipped region in the alignment.
The reference of Arabidopsis thaliana is CRR302668.
The used command is minimap2 -ax map-hifi $ref $reads > $alnsam
Two .sam files:
rd1 0 GWHBDNP00000001.1 15479094 45 2557S9M1D419M1I276M1D211M1D5M1D141M2D73M1I139M1D44M1D294M1D172M1D156M1D217M1D171M1D26M1D447M1D129M1D70M1D205M1D149M1D64M1D55M1D233M1D47M1D306M1D360M1I102M1D289M1D395M1D308M1D122M1D1065M1D367M1D166M1D33M1D24M1I58M1D57M1D535M1D43M1D14M1D20M1D121M1D354M1I77M1D95M1D55M1D120M1D40M1D168M1D47M1D254M1D43M1D225M1D105M1D715M1D19M1D50M1D74M1D286M1I121M1D167M1D335M1D714M1D39M1D195M1D91M1D66M1D217M1D307M1D132M1I88M1D74M1D7M1D15M1D6M1D101M1D432M1D19M1D35M1D373M1D78M1D132M1D68M1D35M1D166M2D142M1D42M1D336M2D11M1D84M1D83M1D142M1I75M1D1098M1D20M1D48M1D34M1D93M1D39M1D200M1D21M1D7M1D300M1D25M1D521M1D190M2D104M1D103M1D137M1D79M1D40M1D145M1D209M2D415M1D42M1D129M1D257M1D137M1D8M1D78M * 0 0
rd1 0 GWHBDNP00000001.1 15476531 30 94M1D487M1D196M1D613M1D350M1D449M1I5M1D51M1D320M1D419M1I276M1D211M1D5M1D141M2D73M1I139M1D44M1D294M1D172M1D156M1D217M1D171M1D26M1D447M1D129M1D70M1D205M1D149M1D64M1D55M1D233M1D47M1D306M1D360M1I102M1D289M1D395M1D308M1D122M1D1065M1D367M1D166M1D33M1D24M1I58M1D57M1D535M1D43M1D14M1D20M1D121M1D354M1I77M1D95M1D55M1D120M1D40M1D168M1D47M1D254M1D43M1D225M1D105M1D715M1D19M1D50M1D74M1D286M1I121M1D167M1D335M1D714M1D39M1D195M1D91M1D66M1D217M1D307M1D132M1I88M1D74M1D7M1D15M1D6M1D101M1D432M1D19M1D35M1D373M1D78M1D132M1D68M1D35M1D166M2D142M1D42M1D336M2D11M1D84M1D83M1D142M1I75M1D1098M1D20M1D48M1D34M1D93M1D39M1D200M1D21M1D7M1D300M1D25M1D521M1D190M2D104M1D103M1D137M1D79M1D40M1D145M1D209M2D415M1D42M1D129M1D257M1D137M1D8M1D78M * 0 0
The read is attached as a .txt file since .fa files are not allowed for upload here: read.txt
Thank you so much for your time and assistance with this issue!
Hi there,
I encountered a confusing mapping issue with minimap2 when aligning a HiFi read from a tandem repeat region of Arabidopsis thaliana chromosome 1 (Chr1):
When aligning to the complete genome reference (all chromosomes): the read maps to Chr1 correctly with normal/negligible soft-clipping.
When aligning to the Chr1-only reference (extracted from the complete genome): the same read shows an unusually long soft-clipped region in the alignment.
The reference of Arabidopsis thaliana is CRR302668.
The used command is
minimap2 -ax map-hifi $ref $reads > $alnsamTwo .sam files:
rd1 0 GWHBDNP00000001.1 15479094 45 2557S9M1D419M1I276M1D211M1D5M1D141M2D73M1I139M1D44M1D294M1D172M1D156M1D217M1D171M1D26M1D447M1D129M1D70M1D205M1D149M1D64M1D55M1D233M1D47M1D306M1D360M1I102M1D289M1D395M1D308M1D122M1D1065M1D367M1D166M1D33M1D24M1I58M1D57M1D535M1D43M1D14M1D20M1D121M1D354M1I77M1D95M1D55M1D120M1D40M1D168M1D47M1D254M1D43M1D225M1D105M1D715M1D19M1D50M1D74M1D286M1I121M1D167M1D335M1D714M1D39M1D195M1D91M1D66M1D217M1D307M1D132M1I88M1D74M1D7M1D15M1D6M1D101M1D432M1D19M1D35M1D373M1D78M1D132M1D68M1D35M1D166M2D142M1D42M1D336M2D11M1D84M1D83M1D142M1I75M1D1098M1D20M1D48M1D34M1D93M1D39M1D200M1D21M1D7M1D300M1D25M1D521M1D190M2D104M1D103M1D137M1D79M1D40M1D145M1D209M2D415M1D42M1D129M1D257M1D137M1D8M1D78M * 0 0rd1 0 GWHBDNP00000001.1 15476531 30 94M1D487M1D196M1D613M1D350M1D449M1I5M1D51M1D320M1D419M1I276M1D211M1D5M1D141M2D73M1I139M1D44M1D294M1D172M1D156M1D217M1D171M1D26M1D447M1D129M1D70M1D205M1D149M1D64M1D55M1D233M1D47M1D306M1D360M1I102M1D289M1D395M1D308M1D122M1D1065M1D367M1D166M1D33M1D24M1I58M1D57M1D535M1D43M1D14M1D20M1D121M1D354M1I77M1D95M1D55M1D120M1D40M1D168M1D47M1D254M1D43M1D225M1D105M1D715M1D19M1D50M1D74M1D286M1I121M1D167M1D335M1D714M1D39M1D195M1D91M1D66M1D217M1D307M1D132M1I88M1D74M1D7M1D15M1D6M1D101M1D432M1D19M1D35M1D373M1D78M1D132M1D68M1D35M1D166M2D142M1D42M1D336M2D11M1D84M1D83M1D142M1I75M1D1098M1D20M1D48M1D34M1D93M1D39M1D200M1D21M1D7M1D300M1D25M1D521M1D190M2D104M1D103M1D137M1D79M1D40M1D145M1D209M2D415M1D42M1D129M1D257M1D137M1D8M1D78M * 0 0The read is attached as a .txt file since .fa files are not allowed for upload here: read.txt
Thank you so much for your time and assistance with this issue!