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Hello,
I keep getting this runtime error when using kb count to generate unspliced and spliced count arrays. Note that I used kb ref previously to generate the necessary files using the genome.fa a…
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Hello,
I have .bam file of paired reads that was pre-filtered to specific locus using samtools (ie.):
`samtools view -bS possorted_genome_bam.bam -f 2 -F 4 "14:21621800-22552200" "7:142299100-14…
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### Description of the bug
Hi,
I tested the pipeline using a cluster configured to use **Kubernetes**.
The multiqc is unable to find the `multiqc_config.yml`
### Command used and terminal ou…
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### Description of the bug
Perhaps fasta needs to be a "required" parameter, that is, perhaps the pipeline should fail immediately if the fasta paramenter isn't set to an (existing) fasta-file?
…
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Hi,
Thanks for developing this tool. When I downloaded bamtofastq_linux to my Linux system, I don't know how to make it work.
My code is "**export PATH=/home/pc/bamtofastq_linux:$PATH、chmod 700 bam…
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--Hi,
strange error using bam2fastq:
BIOBAMBAM/bin/bamtofastq filename=D1_sorted.bam inputformat=bam gz=1 F=D1_R1.fastq.gz F2=D1_R2.fastq.gz O=orphan_D1_1.fastq.gz O2=orphan_D1_2.fastq.gz
BAM…
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Hello,
I found an issue regarding bamtofastq in bedtools (v2.30.0). When I convert a bam file into a fastq file, it seems to create duplicate reads. You can see that there are duplicate read in the…
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Hi,
When I apply bamtofastq to a bam file (illumina single-end reads aligned with STAR), I do get duplicated reads in the fastq.
Checking the former version - 2.29.2 - it works as expected (with…
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Hi,
I was converting a pbio ubam file to fastq like so:
bamToFastq -i input.bam -fq test.fastq
and noticed that all records are repeated twice in the fastq.
for example:
# shows twic…
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Dear Sir/Madam,
Hope you are well.
I download the original bam file and did a bamtofastq convert. So I found that SRR7092170 has a bam. file (link: https://trace.ncbi.nlm.nih.gov/Traces/?view=r…