Bedtools fastafrombed output

lwhitmore · 06-19-2014, 09:19 AM

Hey Everyone, I had a quick question about my bedtools fastafrombed output. When I get a sequence it contains both capital and lowercase letters. Does anyone know why it does this or what it means??

Here is an example
>chr1:157917-159078
ATAAGGAAGAATTATGGAGAATTTAAAAATCTATGCTATTTATAGGCACCTAGTAACAGCTCAGTAAATATTAGCTGCTACTATTATTATTTTTATGGTAATTTCACTCAATTAAAAACTGTCGTTAAAAATTGCCATTGTCATGGAACATAATGTCTCCTACTGTATAATTGTAGAAACAGATACAATttgtcccttggtatatggggggattagttccagctctcccatttctgtgtataccaaaatccacgcatactcaagttttcaaagtcagtcctgtggaatccacatataACACAAATGGGaaaattagtgaggtgtggtgacaagcacctgtagtcccagctacttgtgaggctgaggcaggaggattgcttgagcccaggaggttgaggctgcagtgagccataattgcaccactacactccagtctgggcaacagagtgagacAGAAGGTTGACTTTTTAATAGAATTTTTCTGTTCACTTGAAGATATGGTCAGGATTGTGGCATATGAAAATTCTTCATAAAATAACTATCTAATCCAATTAATGCTGGAATTGGGAACAGCAGAAGTGTCATCTCAGAGCTACTCGCAATGAAAGGTGATGTCTGGGGCTCAGGTGTGTTGAGGTCCCCATGCCTGGACTATGGGTGCTGAGTGGGATTTACTTGTCCATCCATTTTCTATATTCCAGCACTGGGAAACTAGGGACAGTACTTGTTCTCAAGGGAATCTTCAGCTTAGGTGGCTCTGTAAAAGAGAAATTACATCATTGAAAAATCGTCGCAggtcaggtgaggtggctcatacctataatcccagcccactgggagactaaggcaggaggattccgtgaggccaggagttcaagaccagcctgagcaacacagtgaaacctcatctctacaaaaaattagaaaatgaactgggtgcggtaaaacattcgtatagtcccagctactctggaggctgaaataggaggatcgcttgagcccaggaagtggaagctgcagtgagctctgatctcaccactgcactctagccttggtgacagagtgagaccctgtctcaaGacacacacaaacacacacacacacacacacacacCCCCAATCTCACTCTGTCCAGCCTTGACTAATCAAAAGGGCCTTCTG

Thanks
Leanne

GenoMax · 06-19-2014, 09:37 AM

This could be reflective of exons in upper case and introns in lower case sequence, provided it was encoded that way. Something to check on.

WhatsOEver · 06-20-2014, 12:38 AM

These are so-called soft-clipped repetitive regions.
All lower case characters are thereby representing the repeats.

You can reproduce this output using e.g. the Ensembl browser:
-Input your coordinates
-Click "Export Data" on the left
-Choose repeat masked(soft) under fasta options (you will also find the possibility to create a hard clipped version there which will output all lower case characters as 'N')

lwhitmore · 06-20-2014, 09:45 AM

Hey when I try using the ensembl browser no matter which option I choose the sequence that is outputted is on N's

GenoMax · 06-20-2014, 10:06 AM

Quote:

Originally Posted by lwhitmore

Hey when I try using the ensembl browser no matter which option I choose the sequence that is outputted is on N's

Are you sure? I just go this from ensembl browser using your example (and WhatSOever's directions) in original post:

Code:

>1 dna:chromosome chromosome:GRCh37:1:157917:159078:1
AATAAGGAAGAATTATGGAGAATTTAAAAATCTATGCTATTTATAGGCACCTAGTAACAG
CTCAGTAAATATTAGCTGCTACTATTATTATTTTTATGGTAATTTCACTCAATTAAAAAC
TGTCGTTAAAAATTGCCATTGTCATGGAACATAATGTCTCCTACTGTATAATTGTAGAAA
CAGATACAATttgtcccttggtatatggggggattagttccagctctcccatttctgtgt
ataccaaaatccacgcatactcaagttttcaaagtcagtcctgtggaatccacatataAC
ACAAATGGGaaaattagtgaggtgtggtgacaagcacctgtagtcccagctacttgtgag
gctgaggcaggaggattgcttgagcccaggaggttgaggctgcagtgagccataattgca
ccactacactccagtctgggcaacagagtgagacAGAAGGTTGACTTTTTAATAGAATTT
TTCTGTTCACTTGAAGATATGGTCAGGATTGTGGCATATGAAAATTCTTCATAAAATAAC
TATCTAATCCAATTAATGCTGGAATTGGGAACAGCAGAAGTGTCATCTCAGAGCTACTCG
CAATGAAAGGTGATGTCTGGGGCTCAGGTGTGTTGAGGTCCCCATGCCTGGACTATGGGT
GCTGAGTGGGATTTACTTGTCCATCCATTTTCTATATTCCAGCACTGGGAAACTAGGGAC
AGTACTTGTTCTCAAGGGAATCTTCAGCTTAGGTGGCTCTGTAAAAGAGAAATTACATCA
TTGAAAAATCGTCGCAggtcaggtgaggtggctcatacctataatcccagcccactggga
gactaaggcaggaggattccgtgaggccaggagttcaagaccagcctgagcaacacagtg
aaacctcatctctacaaaaaattagaaaatgaactgggtgcggtaaaacattcgtatagt
cccagctactctggaggctgaaataggaggatcgcttgagcccaggaagtggaagctgca
gtgagctctgatctcaccactgcactctagccttggtgacagagtgagaccctgtctcaa
GacacacacaaacacacacacacacacacacacacCCCCAATCTCACTCTGTCCAGCCTT
GACTAATCAAAAGGGCCTTCTG

lwhitmore · 06-20-2014, 10:17 AM

Hey I got it , I guess I wasn't putting in the coordinates correctly

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06-19-2014, 09:19 AM	#1
lwhitmore Member Location: washington Join Date: Aug 2013 Posts: 70	Bedtools fastafrombed output Hey Everyone, I had a quick question about my bedtools fastafrombed output. When I get a sequence it contains both capital and lowercase letters. Does anyone know why it does this or what it means?? Here is an example >chr1:157917-159078 ATAAGGAAGAATTATGGAGAATTTAAAAATCTATGCTATTTATAGGCACCTAGTAACAGCTCAGTAAATATTAGCTGCTACTATTATTATTTTTATGGTAATTTCACTCAATTAAAAACTGTCGTTAAAAATTGCCATTGTCATGGAACATAATGTCTCCTACTGTATAATTGTAGAAACAGATACAATttgtcccttggtatatggggggattagttccagctctcccatttctgtgtataccaaaatccacgcatactcaagttttcaaagtcagtcctgtggaatccacatataACACAAATGGGaaaattagtgaggtgtggtgacaagcacctgtagtcccagctacttgtgaggctgaggcaggaggattgcttgagcccaggaggttgaggctgcagtgagccataattgcaccactacactccagtctgggcaacagagtgagacAGAAGGTTGACTTTTTAATAGAATTTTTCTGTTCACTTGAAGATATGGTCAGGATTGTGGCATATGAAAATTCTTCATAAAATAACTATCTAATCCAATTAATGCTGGAATTGGGAACAGCAGAAGTGTCATCTCAGAGCTACTCGCAATGAAAGGTGATGTCTGGGGCTCAGGTGTGTTGAGGTCCCCATGCCTGGACTATGGGTGCTGAGTGGGATTTACTTGTCCATCCATTTTCTATATTCCAGCACTGGGAAACTAGGGACAGTACTTGTTCTCAAGGGAATCTTCAGCTTAGGTGGCTCTGTAAAAGAGAAATTACATCATTGAAAAATCGTCGCAggtcaggtgaggtggctcatacctataatcccagcccactgggagactaaggcaggaggattccgtgaggccaggagttcaagaccagcctgagcaacacagtgaaacctcatctctacaaaaaattagaaaatgaactgggtgcggtaaaacattcgtatagtcccagctactctggaggctgaaataggaggatcgcttgagcccaggaagtggaagctgcagtgagctctgatctcaccactgcactctagccttggtgacagagtgagaccctgtctcaaGacacacacaaacacacacacacacacacacacacCCCCAATCTCACTCTGTCCAGCCTTGACTAATCAAAAGGGCCTTCTG Thanks Leanne

06-19-2014, 09:37 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,089	This could be reflective of exons in upper case and introns in lower case sequence, provided it was encoded that way. Something to check on.

06-20-2014, 12:38 AM	#3
WhatsOEver Senior Member Location: Germany Join Date: Apr 2012 Posts: 215	These are so-called soft-clipped repetitive regions. All lower case characters are thereby representing the repeats. You can reproduce this output using e.g. the Ensembl browser: -Input your coordinates -Click "Export Data" on the left -Choose repeat masked(soft) under fasta options (you will also find the possibility to create a hard clipped version there which will output all lower case characters as 'N')

06-20-2014, 09:45 AM	#4
lwhitmore Member Location: washington Join Date: Aug 2013 Posts: 70	Hey when I try using the ensembl browser no matter which option I choose the sequence that is outputted is on N's

06-20-2014, 10:17 AM	#6
lwhitmore Member Location: washington Join Date: Aug 2013 Posts: 70	Hey I got it , I guess I wasn't putting in the coordinates correctly