Author Archives: Thomas Cokelaer

format USB key under fedora

I created a bootable USB key and needed to format the key so that others could use it again. Using the format option (see image below) in the KDE file environment, I got this error: This partition cannot be modified … Continue reading

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All about RNA and DNA sequencing

Great entry with description of RNA and DNA sequencing: enseqlopedia

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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

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How to get pypi statistics about package download

A while ago, I designed pypiview, a Python package used to fetch the number of downloads for a package hosted on pypi website. It used to work decently but according to pypi itself the values stored are not reliable and … Continue reading

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How to prevent wget from creating duplicates

wget is used to download file from internet. For instance: wget http://url/test.csvwget http://url/test.csv So far so good but two things may happen. First, you may interrupt the download. Second, you may load the file again. Sometimes, files are huge and … Continue reading

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Meaning of Real, User and Sys time statistics

Under Linux, the time command is quite convenient to get the elapsed time taken by a command call. It is very simple to use: just type your command preceded by the time command itself. For instance: time dftime df The … Continue reading

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git : How to remove a big file wrongly committed

I added a large file to a git repository (102Mb), commited and push and got an error due to size limit limitations on github remote: error: GH001: Large files detected. You may want to try Git Large File Storage – … Continue reading

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git and github : skip password typing with https

if you clone a github repository using the https:// method (instead of ssh), you will have to type your username and passwor all the time. In order to avoid having to type you password all the time, you can use … Continue reading

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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

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How to mount and create a partition on a hard drive dock (fedora)

I got a new hard drive (2.7Tb) but wanted to use it with a docking station. Here are the steps required to use it under my Fedora box. First, I naively went into the Nautilus File Browser hoping to see … Continue reading

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