Question: Metadata error while mapping with bowtie in galaxy
gravatar for aritrancbs.research
5 months ago by
aritrancbs.research10 wrote:

ChIP seq files sequenced in Sanger / illumina 1.9, when processed for mapping with Bowtie for Illumina, showed the following error: "Required metadata values are missing. Some of these values may not be editable by the user. Selecting "Auto-detect" will attempt to fix these values."

Further info said: "Error aligning sequence. Error: reads file does not look like a FASTQ file terminate called after throwing an instance of 'int' /bin/sh: line 1: 9127 Aborted (core dumped) bowtie -q -p 6 -S -n 2 -e 70 -l 28 --maxbts 125 -k 1 -m 1 --phred" Why is it showing this?

While uploading the file through FTP, i had by mistake selected the format type to be Fastq.gz. But later i went to the file attributes and changed the data type to fastqsanger. Is there something to do with this?

For the time being, Metadata is in auto detection mode. But it has been like that for the past 1 hr. What should i do?

chip-seq • 195 views
ADD COMMENTlink modified 5 months ago by valdirbarth0 • written 5 months ago by aritrancbs.research10
gravatar for valdirbarth
5 months ago by
valdirbarth0 wrote:

Can you click on the "view data" button of your fastq file to see if it is in the right format (and maybe paste it here)?

It should look like this:

@NB500989:78:H7WTMBGXY:1:11101:8576:1097 1:N:0:ACTTGA

Is it possible the the first character of your fastq file is a number instead of @?

ADD COMMENTlink modified 5 months ago • written 5 months ago by valdirbarth0
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson24k wrote:

The peak view for a compressed fastq will look like uncompressed. Was the original file .gz compressed or uncompressed? The datatype needs to match the actual content. Reload the data using metadata autodetect if all else fails.

Understanding compressed fastq data (fastq.gz)

Thanks, Jen, Galaxy team

ADD COMMENTlink written 5 months ago by Jennifer Hillman Jackson24k
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