Question: fastq to bam
gravatar for aaltaytas
2.3 years ago by
aaltaytas0 wrote:


I am a newbie in these bioinformatics tools. I have 42 x 2 (paired end) fastq files that got from Illumina Miseq run for Gallus gallus DNA.

I need to convert them into bam files to analyze. I tried to use FastqtoSam converter (gives unaligned bam files) under NGS:Picard for two files for trying but I couldn't do it. Firstly, I selected Illumina (+64) as quality encoding scheme but it gave error. Then I chose Sanger (+33) and it gave bam files which is not opened with IGV (Integrative Genomics Viewer). IGV gives error "An index file is required for SAM&BAM files". I think I did something wrong.

Could you lead me about converting fastq files into bam. Please explain step by step.

Thank you in advance.

bam • 2.8k views
ADD COMMENTlink modified 10 months ago by fp2150 • written 2.3 years ago by aaltaytas0
gravatar for Jennifer Hillman Jackson
2.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:


You seem very close to having this working. Try assigning the "database" metadata attribute to the input datasets. This is required for many tools, especially most in the Samtools and Picard tools groups, along with others - when in doubt or errors occur, set the database to see if issues resolve.

This can be done one dataset at a time after upload (somewhat tedious for so many datasets). Read this is you are using a Custom Reference Genome to learn how to create a Custom Build that can be assigned as a "database" (with this method or the one below)

Or, assign "database" to one dataset at a time or in batch with the Upload tool. The first graphic shows the assignment for one dataset, the second show how to assigned for multiple uploaded datasets that are still queued (meaning: added to the Upload queue, yet not added to the history yet).

Hopefully this helps! Jen, Galaxy team

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by Jennifer Hillman Jackson25k
gravatar for bryantl
2.3 years ago by
United States
bryantl90 wrote:

Try using Fastq Groomer on your fastq files before mapping. This will ensure that your files are in the correct format. Assigning the quality encoding scheme if you do not know it is correct does result in errors.

For the next steps you might find this helpful:

ADD COMMENTlink written 2.3 years ago by bryantl90

Agree, this is always a good check. Help for determining and adjusting fastq quality score scaling is here:

ADD REPLYlink written 2.3 years ago by Jennifer Hillman Jackson25k
gravatar for fp215
10 months ago by
fp2150 wrote:

It sounds to me as though you just need to index the BAM files you produced (IGV won't work with unindexed BAMs)?:

ADD COMMENTlink modified 10 months ago • written 10 months ago by fp2150
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