fastq file with "." in sequence line

zinky · 12-20-2012, 06:03 PM

hi everyone ,
my fastq file contains sequence with "." in it like:
@

TTTAA.GAATAATAAGTCTAATCCCCTTCTATTCTGTAGCACCACTTCGGACAGGGAAGTTAAAGATTCTTCTAATTTGGTTATAGACTGTTCTATAGTT
+
Z\_`a@QQ[Y[Qb^bfa_ghd_[deZbaebecffhhfeddeeddebeec_Z__abbbec\_d]\_c_R`bdd]]c^H^]cZ_`bcaaaa``a_`ZZTTZ_
@
CGAGTGCTGCCGGTCTCCTACGGGAGCAAGTGGCGCAGCTCAAGCAGAAGGTCATGACCCATGTCCGCCACGGCTGCCAGCTGCTGCCAGGGCCTAACGA
+
___cccecgege^[bdgf`aefadU^cebgXcdf^eag`cgfdbR\cgR\\V\HV^b_b`aZ]GGGKKGKKWWTEOQWSGGGJRGJYGGGGEGJGGGGGG
@
C.GGAGTGCAGCTCTCACAGCTGGCTGCAACCGGCACTTATCTTAAAGTGAAAGCAGTTTTTCTGTTAACAAGAGACGGGATGGGGGGGACAGGGGGATG
+
\@P``cc^aecaeghb_f]ghefhcaP^ddgfghhhdc[cbgfagXbe[bfgd]_c`_V\d`dddggddcb]_bQ]Z^Y_QFTTXGOOOEHJW^[aEEEG
@1
AACACTCCTAAGGATCAGGGCCCCTGTTATGATTCCTCGGTCTCCAGTGGCGTCCAGGGTGCCACACCGGGGGGGCGATGCAACCCCCTGGCCTTAGAAT
+
_bbeceeefgggghhiichfhiihiihhhhiiiihiiiihZe`ghdgff_gfafghfhe\bZaadeV`[_]accEOXTTX[GY_`]_aXW^P[R]_bY`b
@
C.CTCCTATACTTTAAAGGATTATGTATTTAAGGAGCTCCAGCGAGACTGG.CAGGTTACAGTGAGACAGACAGACAGACATTGGATTTGGTGCTCTCTA
+
b@P\acc`gggggfaaaghffefhh^cghfffhghhhhfhhffffh[ehhf@LL[__\e_f_\dbg`dbbdaecbXZ]`Z\_RZGZGZbb_[^b]T]Y`G
@
ATAGATGTCTGGACTCTCTTAAATGGAAACAAAGATGACTTCCTCATCTATGACAGATGTGGCCGTCTTGGGTATCACCTTGGGTTGCCTTACTCCTTCC
+
_ZZa^ccc^^e]b`acafad[bcga[^edgf`fg`XYbfg_a^ef]eg]cgdS^a^cghc`gfbaff_Z\HGLH\VV`_ZZ^]GTZW\]]]Z`RTYY_T]

for some reason , machine numbers were masked
at beginning of red sequences above ,there are "." in it . and i hava no idea what it is . so anyone can explain it and give an advice on how to deal with reads like that. thanks a lot

zinky · 12-20-2012, 06:38 PM

o i know "." means N .......

sklages · 12-28-2012, 03:01 AM

... what usually happens with home-made converters qseq-to-fastq ...

swbarnes2 · 01-01-2013, 02:34 PM

use sed to change all the '.' to 'N'

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12-20-2012, 06:03 PM	#1
zinky Member Location: china Join Date: Dec 2011 Posts: 48	fastq file with "." in sequence line hi everyone , my fastq file contains sequence with "." in it like: @ TTTAA.GAATAATAAGTCTAATCCCCTTCTATTCTGTAGCACCACTTCGGACAGGGAAGTTAAAGATTCTTCTAATTTGGTTATAGACTGTTCTATAGTT + Z\_`a@QQ[Y[Qb^bfa_ghd_[deZbaebecffhhfeddeeddebeec_Z__abbbec\_d]\_c_R`bdd]]c^H^]cZ_`bcaaaa``a_`ZZTTZ_ @ CGAGTGCTGCCGGTCTCCTACGGGAGCAAGTGGCGCAGCTCAAGCAGAAGGTCATGACCCATGTCCGCCACGGCTGCCAGCTGCTGCCAGGGCCTAACGA + ___cccecgege^[bdgf`aefadU^cebgXcdf^eag`cgfdbR\cgR\\V\HV^b_b`aZ]GGGKKGKKWWTEOQWSGGGJRGJYGGGGEGJGGGGGG @ C.GGAGTGCAGCTCTCACAGCTGGCTGCAACCGGCACTTATCTTAAAGTGAAAGCAGTTTTTCTGTTAACAAGAGACGGGATGGGGGGGACAGGGGGATG + \@P``cc^aecaeghb_f]ghefhcaP^ddgfghhhdc[cbgfagXbe[bfgd]_c`_V\d`dddggddcb]_bQ]Z^Y_QFTTXGOOOEHJW^[aEEEG @1 AACACTCCTAAGGATCAGGGCCCCTGTTATGATTCCTCGGTCTCCAGTGGCGTCCAGGGTGCCACACCGGGGGGGCGATGCAACCCCCTGGCCTTAGAAT + _bbeceeefgggghhiichfhiihiihhhhiiiihiiiihZe`ghdgff_gfafghfhe\bZaadeV`[_]accEOXTTX[GY_`]_aXW^P[R]_bY`b @ C.CTCCTATACTTTAAAGGATTATGTATTTAAGGAGCTCCAGCGAGACTGG.CAGGTTACAGTGAGACAGACAGACAGACATTGGATTTGGTGCTCTCTA + b@P\acc`gggggfaaaghffefhh^cghfffhghhhhfhhffffh[ehhf@LL[__\e_f_\dbg`dbbdaecbXZ]`Z\_RZGZGZbb_[^b]T]Y`G @ ATAGATGTCTGGACTCTCTTAAATGGAAACAAAGATGACTTCCTCATCTATGACAGATGTGGCCGTCTTGGGTATCACCTTGGGTTGCCTTACTCCTTCC + _ZZa^ccc^^e]b`acafad[bcga[^edgf`fg`XYbfg_a^ef]eg]cgdS^a^cghc`gfbaff_Z\HGLH\VV`_ZZ^]GTZW\]]]Z`RTYY_T] for some reason , machine numbers were masked at beginning of red sequences above ,there are "." in it . and i hava no idea what it is . so anyone can explain it and give an advice on how to deal with reads like that. thanks a lot Last edited by zinky; 12-20-2012 at 06:56 PM. Reason: mask machine number

12-20-2012, 06:38 PM	#2
zinky Member Location: china Join Date: Dec 2011 Posts: 48	o i know "." means N .......

12-28-2012, 03:01 AM	#3
sklages Senior Member Location: Berlin, DE Join Date: May 2008 Posts: 628	... what usually happens with home-made converters qseq-to-fastq ...

01-01-2013, 02:34 PM	#4
swbarnes2 Senior Member Location: San Diego Join Date: May 2008 Posts: 912	use sed to change all the '.' to 'N'