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[jumphone]

Please try:

cut -f 3 SPRINT_identified_all.res > SPRINT_identified_all.res.col3

bedtools intersect -a SPRINT_identified_all.res.col3 -b wheat.bed -u

[jumphone]

Please try:

cut -f 1,2,3 SPRINT_identified_all.res > SPRINT_identified_all.res.col3

bedtools intersect -a SPRINT_identified_all.res.col3 -b wheat.bed -u

If it doesn’t work, can you send me some lines of your files using Email?

Feng

[jumphone]

Have you tried to use the wheat.bed to annotated other files. Can you change it into a standard BED format file?

[jumphone]

BED file should be TAB delimited.

Demo:

1A 7058 7215 GENE ID STRAND

[jumphone]

Please try to use this bed:

cut -f 1,2,3,4,5,6 wheat.bed > wheat_col6.bed

bedtools intersect -a SPRINT_identified_all.res.col3 -b wheat_col6.bed -wa -wb > output.bed

[jumphone]

Please see

https://github.com/arq5x/bedtools2/issues/656

Maybe you need to sort your two bed files

[jumphone]

Can you try BEDOPS?

bedops --intersect a.bed b.bed > output.bed

[jumphone]

bedmap --echo res.bed gene.bed> mapped.bed

[jumphone]

yes

[jumphone]

wheat_col6.sorted.bed

[jumphone]

Please follow the instruction (https://bedops.readthedocs.io/en/latest/content/reference/statistics/bedmap.html) to adjust the "echo" parameter.

[jumphone]

1. You can write script to solve this problem.

2. Or, you can use the "match" function in EXCEL: https://exceljet.net/excel-functions/excel-match-function

[jumphone]

The most important part of SPRINT is the clustering of duplet editing sites.

You can try to apply SPRINT to identify editing on 16s rRNA.

But I’m not sure about that whether there is “duplet editing sites” on 16s rRNA.

You can change the clustering parameters based on the help manual of SPRINT.

https://github.com/jumphone/SPRINT/blob/master/SPRINT_manual.pdf

[iqraishtiaq]

my question is " SPRINT can be worked on DNA sequence ?? " ???????

[jumphone]

SPRINT is designed for "detecting" editing sites, not "predicting".

If there are duplet DNA editing sites on DNA sequence, SPRINT can detect them.

[jumphone]

You can use this sequence as a reference and then apply SPRINT to your NGS data.

If you don't have NGS data, SPRINT cannot help you.

[jumphone]

Please see https://github.com/jumphone/SPRINT/issues/7

[jumphone]

What kind of species did you analyzed?

You can download the repeat annotation file from: https://sourceforge.net/projects/sprintpy/files/dbRES/.

Feng

[jumphone]

I'm not familiar with the repeat regions of plant.

Maybe you can use SPRINT without using repreat annotation file.

Feng