Question: Alternative for SNP detection other than AutoSNP and QualitySNP
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gravatar for athulvs27
23 months ago by
athulvs2710
athulvs2710 wrote:

can any body help me in suggesting an alternative tool for finding SNP in plants( Colocasia esculenta) other than Quality SNP and Auto SNP. AutoSNP works for me however QualitySNP shows error - Segmentation fault (core dumped)

software error • 484 views
ADD COMMENTlink modified 23 months ago by WouterDeCoster43k • written 23 months ago by athulvs2710

There is no need to SHOUT. I have adapted your title and removed the uppercase characters. In addition, please use sensible tags. As such experts can easily find your question and you'll get better help.

Furthermore, your question would benefit a lot from adding more information. For example it is unclear which data you have and how you obtained it.

ADD REPLYlink modified 23 months ago • written 23 months ago by WouterDeCoster43k

Sorry for the mistakes as I am new into it. Data I used was obtained from SRA database of NCBI ( Accession number SRX290678 ) AutoSNP works well for me, however, Quality SNP frequently shows the above-mentioned error.

ADD REPLYlink written 23 months ago by athulvs2710
bslctcri@bslctcri-HP-Z840-Workstation:~/Pictures/CAP3_with_new_data/QualitySNP22102007original_neew (copy)end_data$ GetnonsySNPfasty availcontigseq allavailcontigseqwithSNP allavailcontigseqwithSNP.fasty
creat :nssnpfastydata
creat :nssnpcodingdata
creat :ssnpfastydata
creat :ssnpcodingdata
creat :contigorfdata
creat :utrsnpdata
creat :indelsnpdata
creat :snptagdata
*************Contig46 len:1783  *************begin to analysis************
query sequence:Contig46 with 3 availhit and get memory for blast
*************Contig86 len:985  *************begin to analysis************
query sequence:Contig86 with 63 availhit and get memory for blast
*******correct orf******
600  orf sign:0 |1: Get good orf,others bad orf
*************Contig211 len:434  *************begin to analysis************
query sequence:Contig211 with 44 availhit and get memory for blast
*************Contig275 len:1450  *************begin to analysis************
query sequence:Contig275 with 12 availhit and get memory for blast
*************Contig286 len:437  *************begin to analysis************
query sequence:Contig286 with 2 availhit and get memory for blast
*************Contig297 len:3217  *************begin to analysis************
query sequence:Contig297 with 24 availhit and get memory for blast
*************Contig381 len:568  *************begin to analysis************
query sequence:Contig381 with 8 availhit and get memory for blast
*************Contig385 len:1293  *************begin to analysis************
query sequence:Contig385 with 115 availhit and get memory for blast
 orf sign:1 |1: Get good orf,others bad orf
Segmentation fault (core dumped)
ADD REPLYlink modified 23 months ago by WouterDeCoster43k • written 23 months ago by athulvs2710

I added markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

101010 Button

ADD REPLYlink written 23 months ago by WouterDeCoster43k

what could be the problem that leads to the ERROR - Segmentation fault (core dumped) in the case of AutoSNP.

ADD REPLYlink written 23 months ago by athulvs2710
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