map2085

scientific notation for large numbers of reads

2

command: `bedtools genomecov -d -g genome.size -ibam in.bam > out.cov` _genome.size_ consists of a single RNA "myRNA", length = 8 kb nucleotides. _in.bam_ contains > 15 million reads aligned to...

split by reference chr = "EOF marker is absent. The input is probably truncated."

2

`bamtools split -in my.bam -stub split -reference` The command completes successfully, but all of the resulting files are all "truncated". `samtools view -c split.REF_chr1.bam ` > [W::bam_hdr_read] EOF marker is...

"Too many open files"

4

I am working with very large data. Gzip FASTQ size = 250 GB . I split the FASTQ file into ~1,200 smaller FASTQ files. I aligned the 1,200 FASTQ files...