Bam to Fasta in galaxy

Question

[Adrienn Tóthpál]

Hi,

I am new in the field of bioinformatics, with basic knowledge only. However, we have some bacterial whole genome in BAM, what I would like to convert to FASTA and upload in the NCBI database. I started using Galaxy, which seems quite understandable to me (so far). Though I am stuck and cannot get a proper Fasta file. Can you send me a step by step tutorial or some advise how to solve this? Thanks a lot!

[Adrienn Tóthpál]

Thanks! I changed it.

[Pierre Lindenbaum]

see BAM to FASTA

Answer 1

[Hussain Ather]

You might want to change this from a Forum to Question.

Converting bam to fasta:

samtools bam2fq input.bam | seqtk seq -A - > output.fasta

Here's some instructions on uploading to galaxy

[WouterDeCoster]

I guess OP wants a reference fasta file, and not a single fasta record per read, right?