Follow me
-
Recent Posts
calendar
April 2025 M T W T F S S 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 Recent Comments
- Stan on python argparse issues with the help argument (TypeError: %o format: a number is required, not dict)
- Cormac on Pandas : how to compare dataframe with None
- LP on AWK: the substr command to select a substring
- jrab on python argparse issues with the help argument (TypeError: %o format: a number is required, not dict)
- How to disable SSL verification for urlretrieve? – Peter's blog on python: certificate verified failed
Archives
Categories
Meta
Tag Archives: samtools
How to select genomic region using samtools
To select a genomic region using samtools, you can use the faidx command. This command is used to index a FASTA file and extract subsequences from it. Here is an example of how to use faidx to select a genomic … Continue reading
missing SAM header with minimap2 and samtools
When using minimap2 to map sequencing reads onto a reference, you can use this kind of command (be careful, this is wrong as you will see later): minimap2 -a -x map-pb test.fastq reference.fasta > minimap.samminimap2 -a -x map-pb test.fastq reference.fasta … Continue reading
failed to convert from cram to bam (parse error CIGAR character)
In order to convert a bioinformatic file from CRAM to BAM format, I naively used the samtools command available on a cluster but got this error: samtools view -T reference.fa -b -o output.bam input.cram [sam_header_read2] 3366 sequences loaded. [sam_read1] reference … Continue reading
