BGI-SOAP

1–30 of 460

Welcome to BGI-SOAP group. The SOAP website is http://soap.genomics.org.cn/

And welcome any question about :

SOAP/SOAP3/SOAPaligner, SOAPdenovo, SOAPindel, SOAPsnv, SOAPsv, SOAPfusion, SOAPfuse, SOAPslice, SOAPsnp
general stuff about Bioinformatics, Genomics, Sequencing , NGS , GWAS
sequence alignment, assembly , analysis, visualization

RULES:

Be nice !
Learn, share and help each other.
This is an open community - not an additional service or support from BGI , so DO NOT request service or product or publish business information.
The last one, the very common one - How to ask question ?

How to ask question - the smart way: http://www.catb.org/~esr/faqs/smart-questions.html
How to ask question intelligently : http://www.wikihow.com/Ask-a-Question-Intelligently
Netiquette Guidelines : http://www.ietf.org/rfc/rfc1855.txt

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ChangYu-BGI, … chiti agarwal8

10/8/21

Fix Bugs in 2bwt-builder

IF YOU find any link let me know or if you have an alternative tool for this ? On Wednesday,

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Fix Bugs in 2bwt-builder

IF YOU find any link let me know or if you have an alternative tool for this ? On Wednesday,

10/8/21

9/22/21

download soap2.21 and soapInDel

Hi there, I need soap2.21 and soapInDel for my analysis, but could not find these. It seems that

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download soap2.21 and soapInDel

Hi there, I need soap2.21 and soapInDel for my analysis, but could not find these. It seems that

9/22/21

3/18/20

generate fasta sequence from assembled reads

I need to generate fastas of the mitochondrial genome for use in software for generating haplotype

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generate fasta sequence from assembled reads

I need to generate fastas of the mitochondrial genome for use in software for generating haplotype

3/18/20

7/23/19

SOAPFuse failing at step s05

Dear All, I am usinf SOAPFusev1.27 to identify gene fusions in a set of 57 samples from RNA-Seq data.

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SOAPFuse failing at step s05

Dear All, I am usinf SOAPFusev1.27 to identify gene fusions in a set of 57 samples from RNA-Seq data.

7/23/19

zhangd...@gmail.com, 谢寅龙(Long Xie)2

3/4/19

Much larger assembly by soapdenovo2

Hi Dezhi, You'd better do a kmer analysis and check if it's a highly duplicated or

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Much larger assembly by soapdenovo2

Hi Dezhi, You'd better do a kmer analysis and check if it's a highly duplicated or

3/4/19

mamtama...@gmail.com

6/20/18

information regarding sequence characterisation

Hello everyone, I figured out the deferentially expressed mode of a target gene in two different

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information regarding sequence characterisation

Hello everyone, I figured out the deferentially expressed mode of a target gene in two different

6/20/18

5/16/18

running SoapFuse via docker

Hello, I found docker image for SoapFuse here: https://hub.docker.com/r/avkitex/soapfuse-ref/ I'm

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running SoapFuse via docker

Hello, I found docker image for SoapFuse here: https://hub.docker.com/r/avkitex/soapfuse-ref/ I'm

5/16/18

3/7/18

SOAPdenovo2 compilation issue

1 Q desc. (which area, which software, which version, which env., what error report) 2 Ways I have

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SOAPdenovo2 compilation issue

1 Q desc. (which area, which software, which version, which env., what error report) 2 Ways I have

3/7/18

Vanessa Varaljay

2/11/18

SOAPdenovo for Illumina MiSeq data?

Hi, I was just wondering if SOAPdenovo was appropriate for use with fungal genome assemblies from

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SOAPdenovo for Illumina MiSeq data?

Hi, I was just wondering if SOAPdenovo was appropriate for use with fungal genome assemblies from

2/11/18

Vanessa Varaljay

2/11/18

soapdenovo MiSeq data

Hi, I was just wondering, can soapdenovo be used to assemble a fungal genome from MiSeq data (v3

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soapdenovo MiSeq data

Hi, I was just wondering, can soapdenovo be used to assemble a fungal genome from MiSeq data (v3

2/11/18

Hari, … phillip kyriakakis5

12/4/17

SOAPdenovo2 assembly problem at contig step

Me too, still not resolved. Anyone figure it out? On Sunday, April 3, 2016 at 12:24:41 AM UTC-7,

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SOAPdenovo2 assembly problem at contig step

Me too, still not resolved. Anyone figure it out? On Sunday, April 3, 2016 at 12:24:41 AM UTC-7,

12/4/17

scott monsma, phillip kyriakakis2

12/4/17

cmp_seq error during Contig stage

I have the same problem. Since this is a new post and I can't find the answer anywhere I suppose

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cmp_seq error during Contig stage

I have the same problem. Since this is a new post and I can't find the answer anywhere I suppose

12/4/17

11/9/17

install Soapaligner

1 Q desc. (which area, which software, which version, which env., what error report) 2 Ways I have

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install Soapaligner

1 Q desc. (which area, which software, which version, which env., what error report) 2 Ways I have

11/9/17

yc21...@gmail.com

10/30/17

about the msort

I used the soap aligner for the alignment. Then I will use the soap snp for the variant calling. When

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about the msort

I used the soap aligner for the alignment. Then I will use the soap snp for the variant calling. When

10/30/17

liuco...@gmail.com, Yifang Tan2

7/4/17

Erro in SOAPfuse-v1.27

It's hard to tell what's wrong with your information provided. The error tells you: Wrong

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Erro in SOAPfuse-v1.27

It's hard to tell what's wrong with your information provided. The error tells you: Wrong

7/4/17

6/26/17

您好，我最近在使用Soapdenovo2 去装配基因组。我跑了之后出错，请帮忙看看。测序数据是双端100bp。十分感激。 config file： max_rd_len=100 [LIB]

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您好，我最近在使用Soapdenovo2 去装配基因组。我跑了之后出错，请帮忙看看。测序数据是双端100bp。十分感激。 config file： max_rd_len=100 [LIB]

6/26/17

6/26/17

ERROR:Time spent on hashing reads: 0s, 0 read(s) processed.

Hi, all, I am trying to use soapdenovo2 to assemble contigs using paired-end reads (100 bp length),

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ERROR:Time spent on hashing reads: 0s, 0 read(s) processed.

Hi, all, I am trying to use soapdenovo2 to assemble contigs using paired-end reads (100 bp length),

6/26/17

fyusufi, … 谢寅龙(Long Xie)16

3/10/17

Segmentation fault in SOAPdenovo multi-kmer

The github I sent you before was the latest version v1.04. Best, Yinlong Xie MGI From: bgi-soap@

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Segmentation fault in SOAPdenovo multi-kmer

The github I sent you before was the latest version v1.04. Best, Yinlong Xie MGI From: bgi-soap@

3/10/17

duranteo...@gmail.com

2/26/17

Licensing question

Hello, While visiting SOAP website I noticed the following mention for SOAPaligner-v2.21: “NOTE: Due

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Licensing question

Hello, While visiting SOAP website I noticed the following mention for SOAPaligner-v2.21: “NOTE: Due

2/26/17

2/13/17

Two mate pair libraries have 0 reads mapped during scaffolding

I think I figured it out, it's the -k parameter which is by default set to the same number as -K

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Two mate pair libraries have 0 reads mapped during scaffolding

I think I figured it out, it's the -k parameter which is by default set to the same number as -K

2/13/17

1/16/17

Additional Information About SOAPdenovo pregraph output file

I am interested in using SOAPdenovo2 to efficiently construct a de Bruijn graph. Has anyone had

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Additional Information About SOAPdenovo pregraph output file

I am interested in using SOAPdenovo2 to efficiently construct a de Bruijn graph. Has anyone had

1/16/17

1/16/17

concatenating sequencing runs to assembly

Hi all, I am new assembling genomes with SOAPdenovo and I have the following question: during the

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concatenating sequencing runs to assembly

Hi all, I am new assembling genomes with SOAPdenovo and I have the following question: during the

1/16/17

1/16/17

SOAPec_v2.01 optional trimming

Hi Everyone, What does optional trimming actually do in SOAPec_v2.01? In the supplementary of Luo et

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SOAPec_v2.01 optional trimming

Hi Everyone, What does optional trimming actually do in SOAPec_v2.01? In the supplementary of Luo et

1/16/17

12/21/16

Question about error message for SOAPfuse

Hi, My name is Suk-Young Yoo and I am Sr. statistical analyst at MD Anderson Cancer Center. Now I am

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Question about error message for SOAPfuse

Hi, My name is Suk-Young Yoo and I am Sr. statistical analyst at MD Anderson Cancer Center. Now I am

12/21/16

12/21/16

SOAPfuse error: WG_PEsoap_is_empty

Hi, I am running SOPEfues for RNAseq data. However, the program stopped and I got an message that

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SOAPfuse error: WG_PEsoap_is_empty

Hi, I am running SOPEfues for RNAseq data. However, the program stopped and I got an message that

12/21/16

12/21/16

SOAPfuse error WG_PEsoap_is_empty

1 Q desc. (which area, which software, which version, which env., what error report) 2 Ways I have

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SOAPfuse error WG_PEsoap_is_empty

1 Q desc. (which area, which software, which version, which env., what error report) 2 Ways I have

12/21/16

9/24/16

aio_return error

1 Q desc. (which area, which software, which version, which env., what error report) 2 Ways I have

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aio_return error

1 Q desc. (which area, which software, which version, which env., what error report) 2 Ways I have

9/24/16

8/19/16

Re: [BGI-SOAP:1240] Digest for bgi-soap@googlegroups.com - 2 updates in 2 topics

Dear SOAP user, If you would like the 3 nodes to be turned into a single shared-memory system of 1.5

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Re: [BGI-SOAP:1240] Digest for bgi-soap@googlegroups.com - 2 updates in 2 topics

Dear SOAP user, If you would like the 3 nodes to be turned into a single shared-memory system of 1.5

8/19/16

lamz1...@163.com, lizh...@genomics.cn5

6/23/16

Is chimeric reads a problem in de novo assembly?

Hi, thanks for your reply and sorry for the delay of reply. I had tried to assembly in these two ways

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Is chimeric reads a problem in de novo assembly?

Hi, thanks for your reply and sorry for the delay of reply. I had tried to assembly in these two ways

6/23/16

6/13/16

SOAPdenovo-127mer contig Segmentation fault

I first ran sparse_pregraph like so: SOAPdenovo-127mer sparse_pregraph -s hsapiens.config -K127 -

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SOAPdenovo-127mer contig Segmentation fault

I first ran sparse_pregraph like so: SOAPdenovo-127mer sparse_pregraph -s hsapiens.config -K127 -

6/13/16

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