bs3

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Hi, I installed BS3 according to the instructions, and when I tried checking if it worked, I got an error while trying to run bs3-builder: ~/app/bs3$ ./bs3-build.py -h Traceback (most...

desmodus1984

python3

1

I am having problems configuring it and building a docker container for it, probably due to the antient python2, maybe you can consider moving to python3? I am also confused...

antonkulaga

Error index

2

When I tried to index the genome reference the following error appears: Traceback (most recent call last): File "bs3-build.py", line 5, in from bs_index.wg_build import * File "bs_seeker3/bs_index/wg_build.py", line 49...

lab23UGD

I'm attempting to align a .fq file, containing simulated reads with bisulfite conversion. The file was produced using the tools wgsim [1], for creating the actual reads, and fastx-mutation-tools [2],...

eb-97

bs3 killed and no output

1

Hello! Im trying to use BS-seeker3 for my experiment. Unfortunately, I am getting an error "Loading index from directory... Killed" and also no output is produced despite successful (?) alignment....

AdrianS85

I tried to align fastq-files with BS-Seeker3 but no 1 read was mapped. ``` $ ./bs3-align -1 B213-036-pool_S6_L001_R1_001.fastq -2 B213-036-pool_S6_L001_R2_001.fastq -o B213-036 -f sam -g reference_genome/genome.fa -d reference_genome/ BS-Seeker3 beta...

nmc-ei

BigAllocator: allocating too much memory

2

I am getting the following error when running the paired-end alignment command provided in your markup file. It's c;learly a SNAP error but I want to know if there's a...

Ckhyriem

Can not find the index file in "./reference_genome/Sscrofa11.fa_snap/W_G2A and W_C2T"

4

Hi, I did bs3-build as "./bs3-build -f ./reference_genome/Sscrofa11.fa --aligner=snap". This command went well. However, I can not find the index file in "./reference_genome/Sscrofa11.fa_snap/W_G2A and W_C2T". Thus "./bs3-align.py" said that "Loading...

xiaoxiaolongyuan

bs3-call_methylation gave no results

2

I used bs3-call_methylation with alignment from test data, but got error message as follow, BS-Seeker3 beta [bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files...

k1197445

Hi, these days i analysis methylseq data. and i count bases(C/T, G/A) of target region. but some reads are vanished in output bam file. so i guess, these reads mapped...

jeongmeani