Convert SOLiD fastq to Illumina fastq

[samt]

I want to do this in order to be able to use Bowtie software, but it doesn't support SOLiD data. Is there software to convert it?

[nilshomer]

I want to do this in order to be able to use Bowtie software, but it doesn't support SOLiD data. Is there software to convert it?

If there was a conversion process, it would by definition support SOLiD data. It does not, so if you try to use it, even with double-encoded data, you will get poor results. Try BFAST or BWA for SOLiD data (you could also try SHRiMP).

[samt]

Thanks, will BFAST work on a machine with <3 GBs of memory? (Mapping to whole mouse genome)

[nilshomer]

Thanks, will BFAST work on a machine with <3 GBs of memory? (Mapping to whole mouse genome)

Mouse genome is ~3Gb right? In either case, you will have to split the reference to get it to fit on your machine. This is easy and supported with BFAST, although 3Gb is not very much RAM at all. How many reads, what length, and what computational resources do you have?

[Chipper]

Thanks, will BFAST work on a machine with <3 GBs of memory? (Mapping to whole mouse genome)

BWA should work with < 3Gb and is probably the best choice if resources are limited. Other programs that indexes reads rather than the genome will also work but won't be as fast (MAQ, ZOOM!, SOCS?).

[BENM]

I want to do this in order to be able to use Bowtie software, but it doesn't support SOLiD data. Is there software to convert it?

It is very easy to do that, maybe I can help you, you can reach me at: [email protected]

[ECO]

It is very easy to do that, maybe I can help you, you can reach me at: [email protected]

It's easy to jump off a building, doesn't mean one should.

[samt]

Mouse genome is ~3Gb right? In either case, you will have to split the reference to get it to fit on your machine. This is easy and supported with BFAST, although 3Gb is not very much RAM at all. How many reads, what length, and what computational resources do you have?

~100 million reads, 34 bps (SOliD), I was hoping to use my machine but I have a powerful enough cluster as well.

It seems you are actively still developing BFAST and there isn't much documentation so its hard to tell if it has all the options I will need for the data. I will want to map, assemble and and align back to the genome.

[samt]

It's easy to jump off a building, doesn't mean one should.

I'm not worried about calling SNPS, just obtaining a consensus sequence mapped to the genome. Would converting to NT from CS still be a bad choice?

[nilshomer]

~100 million reads, 34 bps (SOliD), I was hoping to use my machine but I have a powerful enough cluster as well.

It seems you are actively still developing BFAST and there isn't much documentation so its hard to tell if it has all the options I will need for the data. I will want to map, assemble and and align back to the genome.

There is a very complete reference manual that comes with the distribution. Please see download instructions at http://genome.ucla.edu/bfast

[Chipper]

I'm not worried about calling SNPS, just obtaining a consensus sequence mapped to the genome. Would converting to NT from CS still be a bad choice?

Converting will only work as long as you do not have any CS errors (1 CS error will change the rest of the sequence in NT space). The thing with the SOLID is that even with a relatively high CS error rate your mappings will have a very low error rate in NT space due to the 2-base encoding. This is why you need specialised software for the mappings, like BFAST or BWA, else you will get very few alignments.

[BENM]

If your SOLiD FASTQ like this below, you can try this script to convert to Solexa/Illumina FASTQ

@BARB_20071114_2_YorubanMP-BC3_3_16_150_F3
T0220100010131232212020122
+BARB_20071114_2_YorubanMP-BC3_3_16_150_F3
15 21 27 26 24 5 23 18 26 21 11 25 25 19 8 4 25 8 24 7 4 15 18 19 15

[pliang]

Hi BENM,

Thanks for providing the perl script. I am using the SOLiD files from 1000 genome project, and data look like this:

@VAB_Solid0044_20080423_1_Pilot2_YRI_1_8_3KB_MP_11137_718_114
G2203012023131303312303100
+
!611%%(-+%*.&*.,&2,,'%()31

So with your script, the quality line got lost. Just wonder in this case the original quality line can be kept without any change other than removing the first char. I am new to SOLiD data, so want to double check with you. It may be useful for others if you can modify your script to accommodate this format.

Thanks

[BENM]

Hi BENM,

Thanks for providing the perl script. I am using the SOLiD files from 1000 genome project, and data look like this:

@VAB_Solid0044_20080423_1_Pilot2_YRI_1_8_3KB_MP_11137_718_114
G2203012023131303312303100
+
!611%%(-+%*.&*.,&2,,'%()31

So with your script, the quality line got lost. Just wonder in this case the original quality line can be kept without any change other than removing the first char. I am new to SOLiD data, so want to double check with you. It may be useful for others if you can modify your script to accommodate this format.

Thanks

Hi, pliang

Because samt's question is "Convert SOLiD fastq to Illumina fastq", Illumina FASTQ is different from Standard(Sanger) FASTQ in quality format.

The syntax of Solexa/Illumina read format is almost identical to the FASTQ format, but the qualities are scaled differently. Given a character $sq, the following Perl code gives the Phred quality $Q:

$Q = 10 * log(1 + 10 ** (ord($sq) - 64) / 10.0)) / log(10);

The ASCII charactars in Solexa FASTQ means:

CHAR	DEC	QUALITY
A	65	1
B	66	2
C	67	3
D	68	4
E	69	5
F	70	6
G	71	7
H	72	8
I	73	9
J	74	10
K	75	11
L	76	12
M	77	13
N	78	14
O	79	15
P	80	16
Q	81	17
R	82	18
S	83	19
T	84	20
U	85	21
V	86	22
W	87	23
X	88	24
Y	89	25
Z	90	26
[	91	27
\	92	28
]	93	29
^	94	30
_	95	31
`	96	32
a	97	33
b	98	34
c	99	35
d	100	36
e	101	37
f	102	38
g	103	39
h	104	40
;	59	-5
<	60	-4
=	61	-3
>	62	-2
?	63	-1
@	64	0

In contrast to Solexa FASTQ quality, the ASCII characters in standard (sanger) FASTQ, it used to denote:

CHAR	DEC	QUALITY
!       0       -64
!       1       -63
!       2       -62
!       3       -61
!       4       -60
!       5       -59
!       6       -58
!       7       -57
!       8       -56
!       9       -55
!       10      -54
!       11      -53
!       12      -52
!       13      -51
!       14      -50
!       15      -49
!       16      -48
!       17      -47
!       18      -46
!       19      -45
!       20      -44
!       21      -43
!       22      -42
!       23      -41
!       24      -40
!       25      -39
!       26      -38
!       27      -37
!       28      -36
!       29      -35
!       30      -34
!       31      -33
!       32      -32
!       33      -31
!       34      -30
!       35      -29
!       36      -28
!       37      -27
!       38      -26
!       39      -25
!       40      -24
!       41      -23
!       42      -22
!       43      -21
!       44      -20
!       45      -19
!       46      -18
!       47      -17
!       48      -16
!       49      -15
!       50      -14
!       51      -13
!       52      -12
!       53      -11
!       54      -10
"       55      -9
"       56      -8
"       57      -7
"       58      -6
"       59      -5
"       60      -4
#       61      -3
#       62      -2
$       63      -1
$       64      0
%       65      1
%       66      2
&       67      3
&       68      4
'       69      5
(       70      6
)       71      7
*       72      8
+       73      9
+       74      10
,       75      11
-       76      12
.       77      13
/       78      14
0       79      15
1       80      16
2       81      17
3       82      18
4       83      19
5       84      20
6       85      21
7       86      22
8       87      23
9       88      24
:       89      25
;       90      26
<       91      27
=       92      28
>       93      29
?       94      30
@       95      31
A       96      32
B       97      33
C       98      34
D       99      35
E       100     36
F       101     37
G       102     38
H       103     39
I       104     40
J       105     41
K       106     42
L       107     43
M       108     44
N       109     45
O       110     46
P       111     47
Q       112     48
R       113     49
S       114     50
T       115     51
U       116     52
V       117     53
W       118     54
X       119     55
Y       120     56
Z       121     57
[       122     58
\       123     59
]       124     60
^       125     61
_       126     62
`       127     63
a       128     64

So it is easy to conver Solexa->Sanger quality, you just need to build a conversion table in PERL script, just like this:
# Solexa->Sanger quality conversion table
my @conv_table;
for (-64..64) {
$conv_table[$_+64] = chr(int(33 + 10*log(1+10**($_/10.0))/log(10)+.499));
}

I am trying to write a universal script for Solexa/Illumina, SOLiD/ABi, 454/Roche, 3730/Sanger,...transforming to each other format for different purpose, but I need to know your requirements, after that, I will share it to you all.

Hope I answer your question.
BTW I attach the SOLiD2std.pl for your question, just make a little change in SOLiD2Solexa.pl

[pliang]

Hi BENM:

Thank you for response with the new information. It happens that I need to convert the SOLiD color space sequence in fastq to Solexa format for its sequence and quality format. I believe the quality score is already in the AscII scheme (see the copied sequence entry in my first email), that is why I thought that that quality score line can be kept without change for my use. Am I right about this? In any case, I think tool for converting among different format of the data from different platform can be useful for us. Thanks again?