rehamFatima

Hi, I have been trying to index a file using Tabix. I have zipped it using bzip. and the format is : CHRNum start end feature (feature is a CSV...

Thanks @pd3 but I am running command as : `tabix -s 1 -b 2 -e 3 intropolis_test_bz.tsv.gz`

it also says : > [E::hts_idx_push] unsorted positions on sequence #243912249: 1 followed by 0 while we sorted the file using `sort -k 1,1 -k 2,2n`

Thanks Petr, I tried that and got the following output of one line only : `tbx_index_build failed: intropolis_chrGRC38.sorted.NA.tsv.gz`

out/ is generated, but it does not have all the files as listed on your main page. Could you please tell me what data have you used to generate all...

Could you also please tell me which fastqs you have used as part of running the pipeline ? as the data set coming from the `install_genome_data.sh ` only contains fasta...

I have tried running it with different fastqs from various sources, but that crashes down with `Error (modules/align_bowtie2.bds, line 44, pos 3): Bowtie2 index (-bwt2_idx) doesn't exists! (file: .1.bt2 or...

Thanks Jin, yes I have specified `-species mm10` . I have reinstalled the genome data and did see the "success" message. It still does not contain any fastq files. Is...

The command is e.g : `bds atac.bds -species mm10 -se -gensz mm -fastq1 ../genomes/mm10_no_alt_analysis_set_ENCODE.fastq.gz -chrsz ../genomes/mm10/mm10.chrom.sizes` and the output is : ``` Picked up _JAVA_OPTIONS: -Xms8G -Xmx8G -XX:ParallelGCThreads=1 == git...

Thanks Jin, should I send you the output for these ? On 2018-07-02 16:28, Jin Lee wrote: > Please do the following for more info: > ``` > $ cat...