bs3

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Thanks for the wonderful tool to deal with methylation datasets. I wonder whether bs3 is suitable for PBAT library? I noticed that bs2 can handle PBAT datasets. I wonder whether...

zorrodong

Empty sam file

11

hi I used bs3 and every things goes well as follow. But at the end sam file is empty. I found out some other people faced to the same problem....

mrb20045

Sam file is empty afertern aligned reads?

5

Hi, @khuang28jhu when snap aligning reads, everthing seems ok, as below:   as you can see, the align ratio for reads input is high, but the sam...

ChengYunazhi

Large FASTQ's in-core, can exhaust large system RAM

1

I have a server with 256GB of RAM, and two ~127GB FASTQ files. It seems that once you start creating Trimed files, they're entirely in-core, and eventually exhaust system memory....

dakami

Honestly speaking, I'm very pretty interested in your new algorithm. But at now your scripts are not robust enough for use. Since I cloned the scripts and added the PATH...

PhrenoVermouth

SNAP can take unaligned SAM/BAM files as input, which is nice to handle metadata tags that have been added prior to sequencing. It would be good if BS-Seeker3 would expose...

okartal

SNAP version

1

Hi @khuang28jhu , In the README, you said the required version of SNAP is version 1.0beta.23. However, the current release of SNAP is only 1.0beta.18. Best, Kai

ktang

The application output sam format only, the option for bam file exist but wasn't implemented. -f bam doesn't work. The sam file has an error too, Any buddy understand this...

demis001

Memory issue

1

I doubt this is an issue with the snap aligner. Here is the problem, 250G ram, 56 core Linux machine. Out of memory. I did change the temp directory in...

demis001

How to set the number of threads

2

Hi, I am running bs3-align.py and I am wondering if one can set the number of threads to use? Currently it seems that 2 SNAP threads are running. I could...

SchulzLab