Fastq formatting problems

Question: Fastq formatting problems

3.6 years ago by

kchoe • 10

United States

kchoe • 10 wrote:

Hello,

This is my first experience with Galaxy or really any NGS data analysis, so please excuse my ignorance.

I have Illumina Fastq data that I'm trying to run in a C. elegans CloudMap Workflow. I have the workflow and data loaded into Galaxy, but when I click 'run', I can't find my data files in the data loading steps on the next screen. Am I correct to assume that this is a problem with the data format? I'm read that something called Groomer can convert my files if needed, but how do I run this? The first few lines of one of my data files is show below.

Thanks,

Keith

@M02780:50:000000000-AETME:1:1101:20733:1135 2:N:0:1
NATAGCTATGCCGTATNGNNNNTAGCTATGTCGTGTCGTNTATAGCTATGTCGTATCGAATATCGCTCTGTCGTATTGCTANANNNCTTCTACNGNNNCAAATAGGTACGTCGTCCCGNTNATANCTTTGCCTGGCAGTATGTATCNATNNTNNNNAGATAATCCCCATGNNNTANAGATTATAGCAATGCTGCATCGGTCNCANACTAGTCCTATAGTTAGACCACAGCTTCACACTATAAACTCTCCACAAACTACAACACAACGCCTGCACTCTGGCCAAAACACACCCTTTCGACTA
+
#8-8<@FADF-C@FG-#6####,=,,,;C<ECFF;C,;:#::<66CCEC,6CF,C,,,,,,6,;,,:,C,9EDF,:,,,<,#,###,,,,9,,#,###,:,,,,,59,,,:=>+,4?+#+#4++#+:4+4,9,,+,,8,,,,:C,7#+6##+####+++88@,,3,+,,3###6+#+++35,,8,,,,43,,,,1,,**4@#4*#*/***25=7+5++5+2+@*6**82)9C++*+1))+11=*+2+))+/)(((*/))))(,((((../(.(5)())).4(.((.(.48((2.)6((4((
@M02780:50:000000000-AETME:1:1101:20387:1135 2:N:0:1
NATTGAGGAAAATGTANGNNNNCGTCTTGAATCGGTTAGNTTTTGTTTTTCTTTTTTAACTTTTGGAAAGGGTAATTTCTCNTNNNAGGGCAGNTNNNTCAGTCGGTAGTGGTGGCCGNTNGCANTCTGGAGGTCACGAGTTCAAGNCCNNCNNNNCCCCCTAGGTTCACNNNGCNCCTATTGGGAAGTGGAGCAATCCACNACNGGATTATCGGCCACAGTCACCGGCTAGGACGTGACTTAAATTACAGCCCAGAGGGATCACCACCAGGCAGCGGACCTGAATCCCACATCCGACGTG
+
#8BCCGGGGGGGGGGG#=####:=CFGGGGGGGGGCGGG#:CFGGGGGGGGGGGGGGGFFGGGGGGEFGGGGGGGFGGGDG#:###::C@FGG#6###::DDFGGGGGGCGFGGGGG7#:#9:A#+:=FDAFGGCGGGGGFFFGGG#3A##3####88D+>8+@E;@>DE###+6#+6+>@EGFGGGG8EEE,C7,2??=?#*4#49;FGGC?GGG<)?FF**+;;*8>).7AFFE)8)0+;++1;@*67)03(,).,,(-(4::?>BF?:02(:(((-703(4)).).8(,)5:((4(--
@M02780:50:000000000-AETME:1:1101:20976:1135 2:N:0:1
NTCCTCTTGGTGTGAGNANNNNGATCACTTGGTTTTTTANCGATACTCCCGGGTTGCAGTAGGTCAAATCTCTAGTTCCACAANNNTTATCAANANNNTCCAGACTCATTTTCCTATANTNTCGNTATCTTTTTTCAATGCTTTTGNCTNNTNNNNCAAGTTTCCATTTTNNNATNTGCATGCTAATATCATCAATATACCNGGNTAGATCGGAAGAGCGTCGTGCAGGGAAAGAGTGTAGATCTCTGTGGTGGCCGTACCATTAAAAAAAAACAAAGATACGACTATGTTCGACATCATT
+

data format fastq sanger groomer • 962 views

ADD COMMENT • link •

modified 3.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.6 years ago by kchoe • 10

3.6 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The data appears to be of the type Illumina 1.8 or higher, which is labeled as the datatype ".fastqsanger" in Galaxy. To confirm this and properly assign the datatype, please review the help in sections 2.10 and 2.11 on the Support page of the Galaxy wiki, here:
http://wiki.galaxyproject.org/Support

Thanks, Jen, Galaxy team

ADD COMMENT • link written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k

?Thanks. I found the video tutorial right after I submitted my question and I'm running FASTQC now.

Thanks,

Keith

ADD REPLY • link written 3.6 years ago by kchoe • 10

Similar posts • Search »