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bedops sort-bed inconsistencies

sort-bed bedops written 11 months ago by Ram ♦ 32k • updated 11 months ago by Alex Reynolds ♦ 31k

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BEDOPS sort-bed BED_LINE_LEN question

bed bedops intervals sort-bed written 2.4 years ago by rbronste • 380

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Recompile bedops with increased TOKENS_MAX_LENGTH

sort-bed bedops written 3.3 years ago by Ram ♦ 32k • updated 3.3 years ago by Alex Reynolds ♦ 31k

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Recent Replies

C: Cuffmerge Error: Converting GTF files to SAM by sahar.salimi92 • 0
Thanks, my problem is solved.
C: Ignore replacing a comma within quotes by cpad0112 ♦ 15k
is this an xy problem? $ sed -r 's/,/\t/g;s/("\w+)\t/\1 /g' test.txt Name Age "Cit...
A: Extract column which contain <20 exons in a transcript by lessismore • 990
This is really not a bioinformatic question. Anyway, using R, this is the solution. library(...
C: Extract column which contain <20 exons in a transcript by cpad0112 ♦ 15k
use awk, print all the rows where 6th column has values more than or equal to 20 (including colum...
C: How do I know bcftools mpileup command completed? by townsendae • 0
Great! I’ll give that a go, thanks!
C: How do I know bcftools mpileup command completed? by GenoMax ♦ 96k
You would normally use `-o file.out -e file.err` on `sbatch or srun` command line submission (or ...
C: What dataset do I use to annotate a transcriptome? Another transcriptome or a ge by pseudacris • 0
That makes perfect sense, this is very helpful. Thank you very much!
C: Why GATK output haploid GT(genotype) even though my samples are diploid? by haruki • 10
Thank you for your comments. If second individual is missing genotype, it should be "./." beca...
C: RNA-seq ribosomal genes vs proteins by igor ♦ 12k
Good article. Didn't realize they addressed this point so well and that the fractions are consist...
A: How do I know bcftools mpileup command completed? by townsendae • 0
Shoot no I did not. Do you know how I would do that?
C: How do I know bcftools mpileup command completed? by GenoMax ♦ 96k
Hard to tell. This looks like intermediate status output. Did you capture both STDOUT/STDERR to s...
C: Recommendations for genome-wide genotyping platform, array and data analysis sof by GenoMax ♦ 96k
This disorder is likely polygenic? If you have a lot of samples the SNP arrays will be more cost ...

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