Problem converting solid2fastq with Barcode

[m_elena_bioinfo]

Hi NGS users,
I always use solid2fastq 0.6.4e (from bfast+bwa-0.6.4e) to convert csfasta2fastq (both single read and paired end) in this way:

> solid2fastq -o output -b sample_F3.csfasta sample_F5-P2.csfasta sample_F3_QV.qual sample_F5-P2_QV.qual

and it's run perfectly, generating two file (output.read1.fastq and output.read2.fastq)

Now, I have SOLiD samples in PE with barcode.
But when I run

> solid2fastq -o output -b sample_F3_1_23.csfasta sample_F5-BC_1_23.csfasta sample_F3_QV_1_23.qual sample_F5-BC_QV_1_23.qual

the program returns me only a single fastq containing only the reads of F5-BC strands. (output.single.fastq)

How can I fix this problem?
Thanx a lot,
ME

[nilshomer]

Originally Posted by m_elena_bioinfo

Hi NGS users,
I always use solid2fastq 0.6.4e (from bfast+bwa-0.6.4e) to convert csfasta2fastq (both single read and paired end) in this way:

> solid2fastq -o output -b sample_F3.csfasta sample_F5-P2.csfasta sample_F3_QV.qual sample_F5-P2_QV.qual

and it's run perfectly, generating two file (output.read1.fastq and output.read2.fastq)

Now, I have SOLiD samples in PE with barcode.
But when I run

> solid2fastq -o output -b sample_F3_1_23.csfasta sample_F5-BC_1_23.csfasta sample_F3_QV_1_23.qual sample_F5-BC_QV_1_23.qual

the program returns me only a single fastq containing only the reads of F5-BC strands. (output.single.fastq)

How can I fix this problem?
Thanx a lot,
ME

Post your question to bfast-help@lists.sourceforge.net and give the first few reads in both files.

[m_elena_bioinfo]

I posted the question to bfast-help.
These are the reads:

F3_BC.csfasta
>2_62_1595_F3
T33222032200312120022000320022021022000022220300200
>2_63_675_F3
T30223332233222011120303002321220022222232022302223
>2_63_759_F3
T32122302231212321122320322300021031021022202310221
>2_63_1203_F3
T30223300233110010221001112211102131021221222302121
>2_63_1334_F3
T03011300002002020011000212002210033200100001000010
>2_63_1841_F3
T32222332201222021030202202122222222221212222202022
>2_63_1868_F3
T30222102221322320120102022020220101222020220002020

F3_BC_QV
>2_62_1595_F3
8 11 15 11 7 5 4 6 4 13 4 4 7 9 22 4 7 5 5 8 11 4 10 4 4 4 4 12 4 18 4 5 7 14 4 6 4 4 4 12 9 5 7 11 4 10 11 8 6 16
>2_63_675_F3
21 5 5 5 5 9 4 7 10 6 4 6 5 9 6 5 4 8 4 5 12 7 5 6 4 23 6 5 4 7 14 11 4 17 9 8 11 10 8 6 17 8 10 7 4 6 12 9 5 5
>2_63_759_F3
24 4 4 10 9 12 5 4 7 4 7 6 10 10 6 5 4 8 13 4 5 11 5 6 11 19 10 5 5 4 7 4 5 16 8 9 15 10 5 6 13 8 4 5 12 7 13 8 16 13
>2_63_1203_F3
18 4 4 16 9 5 6 6 11 4 16 5 4 4 4 20 6 13 26 4 4 8 8 6 13 17 10 27 17 8 6 15 20 7 8 12 20 19 18 8 8 14 4 4 7 5 5 6 25 19
>2_63_1334_F3
19 30 24 20 21 23 18 28 27 27 16 24 26 13 4 4 20 22 7 5 16 4 23 15 8 19 14 4 19 7 16 6 16 4 5 5 9 15 9 8 5 8 13 7 4 13 16 5 4 8
>2_63_1841_F3
6 4 4 8 5 4 4 4 10 4 12 4 5 10 4 4 4 4 4 4 4 5 7 4 4 12 4 11 7 5 6 4 4 8 11 5 13 6 12 4 4 10 5 9 5 5 7 4 7 8


F5-BC.csfasta
>2_62_1595_F5-BC
G0200102100000300030000103
>2_63_675_F5-BC
G0210222100220203000013012
>2_63_759_F5-BC
G0200112101000213220022013
>2_63_1203_F5-BC
G2200102210020023030013003
>2_63_1334_F5-BC
G0002122002220021030000000
>2_63_1841_F5-BC
G0222112122230212203020122

F5-BC_QV
>2_62_1595_F5-BC
9 5 4 21 7 5 5 6 7 19 19 11 18 4 5 5 14 10 19 8 12 5 20 4 19
>2_63_675_F5-BC
4 25 14 13 8 6 10 7 6 5 4 7 17 4 6 14 11 8 4 10 6 4 9 15 5
>2_63_759_F5-BC
7 31 6 6 18 9 5 10 7 9 6 17 5 5 18 5 4 4 9 4 5 4 10 10 4
>2_63_1203_F5-BC
14 14 8 20 11 10 14 4 5 4 5 5 21 19 6 5 22 15 21 24 18 4 8 8 15
>2_63_1334_F5-BC
5 20 5 9 11 7 32 6 4 4 4 14 18 7 8 4 6 8 14 9 7 14 10 12 11

[seeker]

any progress on this?

[Jorge Amigo]

I don't really see why you have to enter both pairs in a single solid2fastq run, since each pair will output a single fastq file. or does solid2fastq perform any kind of extra check when entering single or paired-end data? wouldn't it be easier to call them separately, ie

solid2fastq -o output sample_F3.csfasta sample_F3_QV.qual
solid2fastq -o output sample_F5-P2.csfasta sample_F5-P2_QV.qual

I also used to use solid2fastq v0.6.4 to convert my SOLiD output, but I never saw that "-b" option, nor even in the current v0.6.5. did it work for you? what exactly was it doing?

[nilshomer]

Originally Posted by Jorge Amigo

I don't really see why you have to enter both pairs in a single solid2fastq run, since each pair will output a single fastq file. or does solid2fastq perform any kind of extra check when entering single or paired-end data? wouldn't it be easier to call them separately, ie

solid2fastq -o output sample_F3.csfasta sample_F3_QV.qual
solid2fastq -o output sample_F5-P2.csfasta sample_F5-P2_QV.qual

I also used to use solid2fastq v0.6.4 to convert my SOLiD output, but I never saw that "-b" option, nor even in the current v0.6.5. did it work for you? what exactly was it doing?

The "-b" option is in the bfast+bwa-0.6.4e version.

[Brajbio]

Hi I have bwa-0.5.9/solid2fastq.pl version. I have two files SolF3.csfasta & SolF3_QV.qual which i want to convert in 'fastq'. After running the command as :

perl solid2fastq.pl Sol SolTest

I am getting the file SolTest.single.fastq.gz but with no reads in file after i unzip it, whereas i have good and equivalent amount of reads in my input read (*F3.csfasta) and qual (*F3_QV.qual) file. Can someone explain me the reason if ever stuck in similar problem.


Strange to say the same command is working fine with another set of file.

[Jorge Amigo]

this thread was about using solid2fastq with barcodes, so I would suggest you to open a new thread asking for help. in it, I guess the first thing you would be noticed is that it is much faster to use the C implementation of solid2fastq rather than the perl script, and that the typical usage command would be something like this:

solid2fastq -o SolF3 SolF3.csfasta SolF3_QV.qual

which would generate a SolF3.fastq file with all SolF3 reads with their corresponding qualities.