output of bedtools bamtofastq are empty files
2
0
Entering edit mode
5.9 years ago
anon ▴ 50

Hi All,

I would like to convert my bam file to fastq. But after I run bedtools with the sorted bam file, I've got two empty files. What should be wrong? (Or what is the proper way to convert a mapped paired-end bam file to fastq?)

What I tried:

samtools sort -n /pathtothefiles/NA12878.chr1.bam /pathtothefiles/NA12878_chr1.qsort
bedtools bamtofastq -i /pathtothefiles/NA12878_chr1.qsort \
                      -fq aln.end1.fq \
                      -fq2 aln.end2.fq

Thanks in advance!

bamtofastq bam fastq samtools bedtools • 3.4k views
ADD COMMENT
0
Entering edit mode

Samtools doesn't sort files in place, it writes them sorted to a new file. You need something like samtools sort -n foo.bam > name_sorted.bam

ADD REPLY
0
Entering edit mode

sorry, I deleted too much from the inserted command ... I did it properly, like you wrote.

ADD REPLY
0
Entering edit mode

OK, thanks for the update. I've moved my answer to a comment in hopes that someone more familiar with that particular command will answer.

ADD REPLY
0
Entering edit mode

it's fairly possible that you can skip the qsort step, read the file from samtools and execute bedtools next. Also, it's possible that samtools is still running and the files will be available at the end of the run. Do you see the file's size increasing with time? Please edit your post with Code paragraph so we can read more easily. 

ADD REPLY
0
Entering edit mode

I usually use bam2fq instead of bedtools, did you try the following?

htscmd bamshuf -uOn 128 aln_reads.bam tmp > shuffled_reads.bam 
htscmd bam2fq -a shuffled_reads.bam > interleaved_reads.fq 
gzip interleaved_reads.fq

In one line:

tscmd bamshuf -uOn 128 aln_reads.bam tmp | htscmd bam2fq -a - | gzip > interleaved_reads.fq.gz 
ADD REPLY
0
Entering edit mode

thanks, I tried, but so far I didn't find a right way to deinterleave the output fastq, or at least the script, which I tried was not correct.

I'm sure that samtools ended before I started to use bedtools, but I try again.

ADD REPLY
0
Entering edit mode
3.5 years ago

I know this post is old but I had the same issue. I was wondering if my data were paired-end or single-end. To do so I tried Bedtools but the resulting files were empty. So, I tried Picard with the paired-end command and it turned out that all my reads went to the unpaired file. Therefore my dataset was single-end and that's probably why the Bedtools command wouldn't work.

ADD COMMENT
0
Entering edit mode

Please cite your command when you mention one in your solution, so that future users can see and better understand. (picard-tools : which command ? which flags ?)

ADD REPLY
0
Entering edit mode
20 months ago

I had the same issue as well. Just found out that the problem stems from sorting. I skipped the sorting step and directly convert the unsorted bam file into fastq file. It worked!

ADD COMMENT
0
Entering edit mode

I tried what you suggested, it is still empty...

ADD REPLY

Login before adding your answer.

Traffic: 2107 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6