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What Does Lowercase Base Mean?(The Result From Samtools Pileup Output)

By running the command:

samtools pileup -cf ref.fa aln.bam | samtools.pl pileup2fq -D100 > cns.fastq

I found that there are a lot of lowercase base such as agctn. So the fastq file is a a mixture of upper case bases and lowercase bases! Does it mean lowercase base letter have a poor quality?Should they be discarded or translated to upper case? If I am am going to discard them, what option or method?

Thanks.

Updated per suggestion.

samtools fastq
• 4,671 views • link
updated by brentp brentp • written by Love • Love

Can you (or someone else) please edit this question so as (1) it says "lowercase base" not "lower base" and (2) the title is meaningful (i.e. it mentions samtools pileup output). I'd do it myself but it's better if people learn to improve their own questions.

• 0 views • link
written by Neilfws Neilfws

@neilfws, what do you mean wit improving the question?, it couldn't be clearer

• 0 views • link
written by Raygozak Raygozak

1 answer

The output from the pileup matches the case in your fasta. So your ref.fa must have mixed case.

• 1 views • link
written by brentp brentp

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