[IGBF-3741] Align Trinity Contigs to SL4 & SL5 via BLAT - JIRA UNCC

Details

Type: Task
Status: Closed (View Workflow)
Priority: Minor
Resolution: Done
Affects Version/s: None
Fix Version/s: None
Labels:
None

Story Points:
2
Epic Link:
Support NSF pollen grant
Sprint:
Summer 1

Description

Goal is to visualize how the BLAT alignments look.
To do this we need to align contigs to SL4 and SL5 genome (and not to CDS).

But before we do this, we want to implement Ann's suggestions for blat parameters. (e.g., max intron size:10K)

The current blat command being used is this:

blat /projects/tomato_genome/db/SL5/SL5.cds.fa \
/dev/null /dev/null -tileSize=11 -makeOoc=$

{file}

.11.ooc -repMatch=1024

Script will point to proper reference genome files.
And we will incorporate other parameters as Ann suggests.
which are..........

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Robert Reid created issue - 21/May/24 11:17 AM

Robert Reid made changes - 21/May/24 11:17 AM

Field	Original Value	New Value
Epic Link		IGBF-2993 [ 21429 ]

Robert Reid made changes - 21/May/24 11:17 AM

Description	Goal is to visualize how the BLAT alignments look. To do this we need to align contigs to SL4 and SL5 genome (and not to CDS). But before we do this, we want to implement Ann's suggestions for blat parameters. (e.g., max intron size:10K) The current blat command being used is thisL {quote}blat /projects/tomato_genome/db/SL5/SL5.cds.fa \ /dev/null /dev/null -tileSize=11 -makeOoc=${file}.11.ooc \ -repMatch=1024{quote} Script will point to proper reference genome files. And we will incorporate other parameters as Ann suggests. which are..........	Goal is to visualize how the BLAT alignments look. To do this we need to align contigs to SL4 and SL5 genome (and not to CDS). But before we do this, we want to implement Ann's suggestions for blat parameters. (e.g., max intron size:10K) The current blat command being used is thisL {quote}blat /projects/tomato_genome/db/SL5/SL5.cds.fa \ /dev/null /dev/null -tileSize=11 -makeOoc=${file}.11.ooc \ -repMatch=1024{quote} Script will point to proper reference genome files. And we will incorporate other parameters as Ann suggests. which are..........
Sprint		Spring 10 [ 194 ]

Robert Reid made changes - 21/May/24 11:18 AM

Summary

Align Trinity Contigs to SL$ & SL5 via BLAT

Align Trinity Contigs to SL4 & SL5 via BLAT

Robert Reid made changes - 21/May/24 11:18 AM

Description

Goal is to visualize how the BLAT alignments look.
To do this we need to align contigs to SL4 and SL5 genome (and not to CDS).

But before we do this, we want to implement Ann's suggestions for blat parameters. (e.g., max intron size:10K)

The current blat command being used is thisL

{quote}blat /projects/tomato_genome/db/SL5/SL5.cds.fa \
/dev/null /dev/null -tileSize=11 -makeOoc=${file}.11.ooc \
-repMatch=1024{quote}

Script will point to proper reference genome files.
And we will incorporate other parameters as Ann suggests.
which are..........

Goal is to visualize how the BLAT alignments look.
To do this we need to align contigs to SL4 and SL5 genome (and not to CDS).

But before we do this, we want to implement Ann's suggestions for blat parameters. (e.g., max intron size:10K)

The current blat command being used is thisL

{quote}blat /projects/tomato_genome/db/SL5/SL5.cds.fa \
/dev/null /dev/null -tileSize=11 -makeOoc=${file}.11.ooc \
repMatch=1024 {quote}

Script will point to proper reference genome files.
And we will incorporate other parameters as Ann suggests.
which are..........

Robert Reid made changes - 21/May/24 11:19 AM

Description

Goal is to visualize how the BLAT alignments look.
To do this we need to align contigs to SL4 and SL5 genome (and not to CDS).

But before we do this, we want to implement Ann's suggestions for blat parameters. (e.g., max intron size:10K)

The current blat command being used is thisL

{quote}blat /projects/tomato_genome/db/SL5/SL5.cds.fa \
/dev/null /dev/null -tileSize=11 -makeOoc=${file}.11.ooc \
repMatch=1024 {quote}

Script will point to proper reference genome files.
And we will incorporate other parameters as Ann suggests.
which are..........

Goal is to visualize how the BLAT alignments look.
To do this we need to align contigs to SL4 and SL5 genome (and not to CDS).

But before we do this, we want to implement Ann's suggestions for blat parameters. (e.g., max intron size:10K)

The current blat command being used is thisL

{quote}blat /projects/tomato_genome/db/SL5/SL5.cds.fa \
/dev/null /dev/null -tileSize=11 -makeOoc=${file}.11.ooc -repMatch=1024 {quote}

Script will point to proper reference genome files.
And we will incorporate other parameters as Ann suggests.
which are..........

Robert Reid made changes - 21/May/24 11:20 AM

Description

Goal is to visualize how the BLAT alignments look.
To do this we need to align contigs to SL4 and SL5 genome (and not to CDS).

But before we do this, we want to implement Ann's suggestions for blat parameters. (e.g., max intron size:10K)

The current blat command being used is thisL

{quote}blat /projects/tomato_genome/db/SL5/SL5.cds.fa \
/dev/null /dev/null -tileSize=11 -makeOoc=${file}.11.ooc -repMatch=1024 {quote}

Script will point to proper reference genome files.
And we will incorporate other parameters as Ann suggests.
which are..........

Goal is to visualize how the BLAT alignments look.
To do this we need to align contigs to SL4 and SL5 genome (and not to CDS).

But before we do this, we want to implement Ann's suggestions for blat parameters. (e.g., max intron size:10K)

The current blat command being used is this:

blat /projects/tomato_genome/db/SL5/SL5.cds.fa \
/dev/null /dev/null -tileSize=11 -makeOoc=${file}.11.ooc -repMatch=1024

Script will point to proper reference genome files.
And we will incorporate other parameters as Ann suggests.
which are..........

Ann Loraine made changes - 23/May/24 3:56 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

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Ann Loraine added a comment - 23/May/24 4:19 PM

As requested, here are the parameters and inputs you should use to align the contig sequences against the SL4 and SL5 genome sequences.

You need "target" genome sequence files in ".2bit" format. Please use these files as the target sequences:

SL5 genome assembly, in blat-friendly ".2bit" format: http://lorainelab-quickload.scidas.org/quickload/S_lycopersicum_Jun_2022/S_lycopersicum_Jun_2022.2bit
SL4 genome assembly, in blat-friend ".2bit" format: http://lorainelab-quickload.scidas.org/quickload/S_lycopersicum_Sep_2019/S_lycopersicum_Sep_2019.2bit

The output format you should use for blat is "pslx". This will ensure that the aligned sequence gets included in the output. If we do that, IGB will be able to display the sequence and we can more easily check that the results are good. To specify this output format, use this option: -out=pslx
Please run blat using the option that does not include a header. That option is: -noHead
Do not use the default maximum intron size. It is too big. Use 13,000 bases. That option is: -maxIntron=13000

For more information about running blat, see this link: https://genome.ucsc.edu/goldenPath/help/blatSpec.html

Last but not least, I recommend that you run blat in parallel. If you do that, make sure that you keep track of which sequence came from which collection of assembled contigs. Otherwise, it will be super hard to sanity-check the results. For example, what I would like to do is open up the blat alignments for a set of transcript contigs where I know exactly which RNA-Seq reads were used to make them. Then, I can easily use the Genome Browser to compare the genome alignments for the input RNA-Seq reads to the alignments of their assembled contigs. If we do this, we can easily get an idea for how the trinity assembly software performs when there are lots of reads or not so many reads in a given region. It will make more sense when I can show you what I mean in IGB

Show

Ann Loraine added a comment - 23/May/24 4:19 PM As requested, here are the parameters and inputs you should use to align the contig sequences against the SL4 and SL5 genome sequences. You need "target" genome sequence files in ".2bit" format. Please use these files as the target sequences: SL5 genome assembly, in blat-friendly ".2bit" format: http://lorainelab-quickload.scidas.org/quickload/S_lycopersicum_Jun_2022/S_lycopersicum_Jun_2022.2bit SL4 genome assembly, in blat-friend ".2bit" format: http://lorainelab-quickload.scidas.org/quickload/S_lycopersicum_Sep_2019/S_lycopersicum_Sep_2019.2bit The output format you should use for blat is "pslx". This will ensure that the aligned sequence gets included in the output. If we do that, IGB will be able to display the sequence and we can more easily check that the results are good. To specify this output format, use this option: -out=pslx Please run blat using the option that does not include a header. That option is: -noHead Do not use the default maximum intron size. It is too big. Use 13,000 bases. That option is: -maxIntron=13000 For more information about running blat, see this link: https://genome.ucsc.edu/goldenPath/help/blatSpec.html Last but not least, I recommend that you run blat in parallel. If you do that, make sure that you keep track of which sequence came from which collection of assembled contigs. Otherwise, it will be super hard to sanity-check the results. For example, what I would like to do is open up the blat alignments for a set of transcript contigs where I know exactly which RNA-Seq reads were used to make them. Then, I can easily use the Genome Browser to compare the genome alignments for the input RNA-Seq reads to the alignments of their assembled contigs. If we do this, we can easily get an idea for how the trinity assembly software performs when there are lots of reads or not so many reads in a given region. It will make more sense when I can show you what I mean in IGB

Ann Loraine made changes - 23/May/24 4:19 PM

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Ann Loraine [ aloraine ]

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Ann Loraine added a comment - 23/May/24 4:20 PM

I added the requested details in the preceding comment.
If you have any questions, please let me know.

attn:

Robert Reid
Brandon Bendickson

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Ann Loraine added a comment - 23/May/24 4:20 PM I added the requested details in the preceding comment. If you have any questions, please let me know. attn: Robert Reid Brandon Bendickson

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Ann Loraine added a comment - 23/May/24 4:20 PM

Please note I am moving this to the next sprint since it seems unlikely we will get around to doing further work on this during the current sprint, which ends tomorrow.

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Ann Loraine added a comment - 23/May/24 4:20 PM Please note I am moving this to the next sprint since it seems unlikely we will get around to doing further work on this during the current sprint, which ends tomorrow.

Ann Loraine made changes - 23/May/24 4:20 PM

Sprint

Spring 10 [ 194 ]

Summer 1 [ 195 ]

Robert Reid made changes - 24/May/24 9:27 AM

Assignee

Robert Reid [ robertreid ]

Robert Reid made changes - 03/Jun/24 9:39 AM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Robert Reid made changes - 03/Jun/24 9:39 AM

Assignee

Robert Reid [ robertreid ]

Brandon Benkick [ bbendick ]