output of mite-hunter

[mdayii]

I am now using MITE-hunter, and based on the manual, _Each “Step_8” file contains a TE family, except for two. One is “Step_8.singlet” that contains all TEs that don’t have similar homologs in the output, and the other is “Step_8.paired” that contains putative compound TEs. A compound TE is composed with two different or same TEs and should be excluded._

My question is to get a final consensus file that will be used in downstream analyses, should we combine all Step_8 files including Step_8.singlet and Step_8.paired? Or keeping only one sequence from Step_8.paired file?

[jburnette]

Hi,

Each of the step 8 files represents a different class of TE, so you cannot use them to make a single consensus. The paired file should be ignored.

Dr. Burnette

Jim Burnette, Ph.D. Academic Coordinator University of California, Riverside

Office: 101A Rochelle and Allison Campbell Hall

900 University Ave Riverside, CA 92521 Voicemail: 951-827-5157

On Dec 12, 2020, at 12:07 PM, mdayii notifications@github.com wrote:

I am now using MITE-hunter, and based on the manual, Each “Step_8” file contains a TE family, except for two. One is “Step_8.singlet” that contains all TEs that don’t have similar homologs in the output, and the other is “Step_8.paired” that contains putative compound TEs. A compound TE is composed with two different or same TEs and should be excluded.

My question is to get a final consensus file that will be used in downstream analyses, should we combine all Step_8 files including Step_8.singlet and Step_8.paired? Or keeping only one sequence from Step_8.paired file?

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[mdayii]

Hi Dr. Burnette,

My aim is to get all TEs in a file to combine results of other TEs tools to make a final repeat library of a species and classify by RepeatClassifer and later mask by RepeatMasker.

Is it okay to combine all step8 files except paired one? If not, how can I use them to reach to my aim?

Thank you.

[jburnette]

That should work to combine all into one file.

Jim Burnette, Ph.D. Academic Coordinator University of California, Riverside

Office: 101A Rochelle and Allison Campbell Hall

900 University Ave Riverside, CA 92521 Voicemail: 951-827-5157

On Dec 14, 2020, at 10:41 AM, mdayii notifications@github.com wrote:

Hi Dr. Burnette,

My aim is to get all TEs in a file to combine results of other TEs tools to make a final repeat library of a species and classify by RepeatClassifer and later mask by RepeatMasker.

Is it okay to combine all step8 files except paired one? If not, how can I use them to reach to my aim?

Thank you.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/jburnette/MITE-Hunter/issues/7#issuecomment-744633625, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAD2KLANC6XTCIKWTVK6FHDSUZL7PANCNFSM4UYSL6TQ.

[zhangkaihui1]

I have the same goal as you, but Step_678 has no result, can you help me?

[blastall] ERROR: A_3_11243: BioseqFindFunc: couldn't uncache

[zhangkaihui1]

I am now using MITE-hunter, and based on the manual, _Each “Step_8” file contains a TE family, except for two. One is “Step_8.singlet” that contains all TEs that don’t have similar homologs in the output, and the other is “Step_8.paired” that contains putative compound TEs. A compound TE is composed with two different or same TEs and should be excluded._

My question is to get a final consensus file that will be used in downstream analyses, should we combine all Step_8 files including Step_8.singlet and Step_8.paired? Or keeping only one sequence from Step_8.paired file?

I have the same goal as you, but Step_678 has no result, can you help me?

[blastall] ERROR: A_3_11243: BioseqFindFunc: couldn't uncache