Wouter De Coster
Wouter De Coster
Have you tried installation from (bio)conda?
I was trying the RNA-seq alignment you announced and get a segmentation fault. ``` [00:55:06 ProcessReads] Using 1 threads. [00:55:07 ProcessReads] [CPU time: 0.93 sec, RSS: 246 MB] Read: 640/75299...
I reproduced the segmentation fault using the fastq with just the offending read. But here is the punchline already: I use as genome reference the hg19 igenome & for gtf...
Does ngmlr actually write in BAM format? Is `output.bam` maybe a SAM file? Also, I would suggest you to use `samtools sort output.bam -o sorted.bam` to make sure the output...
That NGMLR help string is actually a mistake, and what you just pasted is the help of `--rg-id`, but that's something that's wrong in the code and should not be...
I would try to take a look at that line, and see if I can spot what's wrong. Is it the last line of the file?
That looks like a very long read. Perhaps you should try alignment with the `--bam-fix` argument
A late follow up on this... I used the following command: (changed path to reference directory) ``` zcat fastq/*.fastq.gz | ngmlr --verbose -x ont -t 48 -r /path/to/dir/withoutwritepermission/genome_hg19.fa | samtools...
And not entirely related: combining --verbose with writing the output to stdout goes bonkers, with the reads eventually ending up on my terminal.
It's not something that I personally have needed already - but I can see some value in it. I can imagine that you want to know the coverage obtained from...