fastx_toolkit can't work

[ishmael]

Just curious, I googled the unique machine id: hwi-st298.
And I found this:
http://seqanswers.com/forums/showthread.php?t=15928
It looks that the company triggered the malformation not the first time.
Which company it is? BGI?

[arvid]

they come from a seqencing company,i didn't convert them.but when i convert them to Illumina fastq,their ASCII values is also malformed,what can i do?

Ask the company what they did to create such data..?

[letusgo]

O.K. I missed this before. Clearly your quality lines are malformed; are these after you converted them? You have ASCII values ranging from 35 (#) to 105 (i). No valid FASTQ files for Illumina reads uses a range this wide.

they come from a seqencing company,i didn't convert them.but when i convert them to Illumina fastq,their ASCII values is also malformed,what can i do?

[kmcarr]

@hwi-st298:170:81mg3abxx:1:1101:1349:2455 1:n:0:ttaggc
ctggttcagccttcttaggctcttcttctgtttccttacctcagatcggaagagcacacgtctgaactccagtcacttaggcatttcgtatgacgtatgt
+
cccfffffghghfhgiijjfhegi?fhiihfchggggcegggicgebchfhgdhgiiibaf@fh7@@e;7=a;aadd>ccbcca################
@hwi-st298:170:81mg3abxx:1:1101:1372:2461 1:n:0:ttaggc
agacggtgttgcataagctgttgtatctgttgctgttgaaactgaaactgctgctgttgctgcttttgttttttagatcggcagggcacacgtgtgcgac
+
@@@fff@dfhgff<gaeehggg@@ehafhiiibgg<?ff<?<bf<fg@gg?be<<3?88bf#######################################
@hwi-st298:170:81mg3abxx:1:1101:1866:2486 1:n:0:ttaggc
gtcactttgtacctcttctcaaattaggaaaatacgaagttcgaggaacgcctttcgttctctttttttcttggtcggcagggtcagggcctttcttgct
+
@@cdffffdddhhegeggeegeh>hhhiigiij>ffcgggeghid0?dfdfggiig1=;;ceggcac<<ce@a@>>>;??>95(9<(38<?<a#######

O.K. I missed this before. Clearly your quality lines are malformed; are these after you converted them? You have ASCII values ranging from 35 (#) to 105 (i). No valid FASTQ files for Illumina reads uses a range this wide.

[letusgo]

I always thought it was -Q33... Does -Q 33 work?

[edit] Oh, yes, it does.

unfortunately,it doesn't work for my fastq files,then i convert the sanger fastq to illumina fastq.when i run fastq_quality_filter,another error :

fastq_quality_filter: Invalid quality score value (char 'i' ord 105 quality value 41) on line 4

[kmcarr]

i add this option ,but another error is happened like:

fastq_quality_filter: Invalid quality score value (char 'J' ord 74 quality value 41) on line 4

letusgo,

Are you sure that you are using v. 0.0.13? See this response to a thread about this issue from last year. (Hint, try searching the forum first, your question may already have been answered.) Using v. 0.0.13 and the '-Q 33' option together should work. If it doesn't then your FASTQ file may be malformed.

[letusgo]

can you post a few (12) lines of your fastq file?

@hwi-st298:170:81mg3abxx:1:1101:1349:2455 1:n:0:ttaggc
ctggttcagccttcttaggctcttcttctgtttccttacctcagatcggaagagcacacgtctgaactccagtcacttaggcatttcgtatgacgtatgt
+
cccfffffghghfhgiijjfhegi?fhiihfchggggcegggicgebchfhgdhgiiibaf@fh7@@e;7=a;aadd>ccbcca################
@hwi-st298:170:81mg3abxx:1:1101:1372:2461 1:n:0:ttaggc
agacggtgttgcataagctgttgtatctgttgctgttgaaactgaaactgctgctgttgctgcttttgttttttagatcggcagggcacacgtgtgcgac
+
@@@fff@dfhgff<gaeehggg@@ehafhiiibgg<?ff<?<bf<fg@gg?be<<3?88bf#######################################
@hwi-st298:170:81mg3abxx:1:1101:1866:2486 1:n:0:ttaggc
gtcactttgtacctcttctcaaattaggaaaatacgaagttcgaggaacgcctttcgttctctttttttcttggtcggcagggtcagggcctttcttgct
+
@@cdffffdddhhegeggeegeh>hhhiigiij>ffcgggeghid0?dfdfggiig1=;;ceggcac<<ce@a@>>>;??>95(9<(38<?<a#######

[mgogol]

I always thought it was -Q33... Does -Q 33 work?

[edit] Oh, yes, it does.

[sisch]

Can you post a few (12) lines of your FastQ file?

[letusgo]

Try the command line option -Q 33 to indicate Sanger phred scores. That option has worked for me in the past

i add this option ,but another error is happened like:

fastq_quality_filter: Invalid quality score value (char 'J' ord 74 quality value 41) on line 4

[letusgo]

The program is using solexa quality scores (starting at 64) instead of sanger (starting at 33). According to the fastx website, support for sanger quality scores was added in version 0.0.13. Which version are you running?

i use the version 0.0.13,but it doesn't work too,how can i convert sanger fastq to illumina fastq format?

[dfjenkins3]

Try the command line option -Q 33 to indicate Sanger phred scores. That option has worked for me in the past

[Alex Renwick]

The program is using solexa quality scores (starting at 64) instead of sanger (starting at 33). According to the fastx website, support for sanger quality scores was added in version 0.0.13. Which version are you running?

[letusgo]

when i use fastx_toolkits ,just like fastq_quality_filter:

$ fastq_quality_filter -q 5 -p 50 -i ./SampleS_1.fq -o ./SampleSfilter_1.fq

unfortunately，it returns as：

fastq_quality_filter: Invalid quality score value (char '#' ord 35 quality value -29) on line 4

how can I solve it ?