Hello everyone, I am new to bioinformatics. I have several files in BAM format and I want to convert them to fastq using samtools.
Is there any way to convert them all at once?
I tried : samtools fastq * .bam > * .fastq but it was failure.
•
written
by
vanessagpds •
1 answer
To process one after another:
for file in *.bam; do samtools fastq $file > ${file//.bam/.fastq}; done
If you want to run them simultaneously (let's say 8 at a time) you need to install the program parallel, then:
for file in *.bam; do echo samtools fastq $file ">" ${file//.bam/.fastq} >> tasks.txt; done
parallel -j 8 -a tasks.txt
Hi e.ortiz.v
Your answer is so helpful. I have a question that
if I have abc.bam and I would like to remove .bam and add nothing and get abs. after that, I will add abs to the string of is it ok to write it in this way
if I just remove and keep the file name
A= test_1.fq.gz -R "@RG\tID:1\tSM:${A[i]//_1.fq.gz}"
result is
-R "@RG\tID:1\tSM: test"
is it correct?
Hi E. Ortiz,
I would like to ask you, please, if would it be possible a similar code for simultaneously to convert many fastq files to respective bam files?. Could you write that code ?. I was trying the above code changing fastq by bam and vice versa, but it doesn't work for me.
Thank you very much.
Log in to answer this question.
-
Fastq to Fasta format
written by taniamahmood38 •
-
Getting nucleotide frequencies per position
written by PluralizesEverythings •
-
Converting multiple cram files to fastq files.
written by Rose •
-
Download multiple SRA samples and convert into fasta format at once
written by twangxxx •
-
Samtools bam2fq converting bam file to fastq. What happens to unmapped reads?
written by williamsbrian5064
-
cram file to fastq conversion
written by erl1977 •
-
FASTQ --> FASTA Conversion
written by Khosh.0 •
-
Compare Fastq files
written by fowler.trentd •
-
How to convert a bam file into tsv file format?
written by malikbashirkhan2 •
-
How to convert to .SRA files to .FQ (FASTQ)
written by Veli Kaan Aydin •
