Question: Error from trimmed fastq file to bam file via bowtie2
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gravatar for franziska.froeb
9 weeks ago by
franziska.froeb0 wrote:

Hello everyone,

I did ChIPseq analyses a couple of times and it always worked quite nicely.

So, now I have the problem that I have fastq files (size 700-1000MB) which I can trim at first without any problems, but after bowtie2 the error message below occurs and my file is below 1KB?!

Error: Read Error: Read SRR619423.17 1_13_196/1 has more quality values than read characters.

Error: Read SRR619423.81 1_22_371/1 has more quality values than read characters.

Error: Read SRR619423.65 1_19_1131/1 has more quality values than read characters.

Can somebody help me what I am doing wrong or what I do have to change to make it work?

Thank you in advance for your help!

fastq qa bowtie datatype content • 77 views
ADD COMMENTlink modified 9 weeks ago by Jennifer Hillman Jackson23k • written 9 weeks ago by franziska.froeb0
0
gravatar for Jennifer Hillman Jackson
9 weeks ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

The fastq data is in color space. The tool Manipulate FASTQ reads on various attributes can be used to transform into a type of nucleotide encoding. How to is explained in the help section of the tool form.

Do this step first - followed by any other downstream tools, including QA tools.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 9 weeks ago by Jennifer Hillman Jackson23k
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