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Results tagged with samtools
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user 4001
Questions specific to interacting with and post-processing sequence alignments using the SAMtools package. For questions specifically about formats SAM, BAM or CRAM use tags sam or bam,
3
votes
1
answer
2k
views
Running htseq-count over BAM files
I have read the htseq-count documentation as well as samtools and figured that the following command should work:
samtools sort -on file.bam | samtools view -h - | htseq-count --type=exon --idattr=gene_id … Just note that the newer versions of htseq-count don't require sorted .bam files and, so following the editing of the .gtf file, all I needed to do was convert it to .sam using samtools view -h and then …
- 910
3
votes
2
answers
316
views
Frequency of specific viral sequence in .BAM or .fastq
So, my question is: if I were to use samtools - or any other program - to convert the .bam files to .fastq, is there any possibility that I could lose such information - e.g. viral seqs - that would have …
M__♦
- 13k
1
vote
2
answers
99
views
Using preprocessing/alignment functions on the server
I have a series of raw RNA sequencing files: .bam and wish to utilize samtools (or others) to begin the data preprocessing steps defined in many workflows. … : -bash-samtools: command not found
When I try to install the package, say samtools, by running sudo apt install samtools, I get an error stating I do not have permission to do such. …
M__♦
- 13k