User: kk.mahsa

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kk.mahsa50
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Posts by kk.mahsa

<prev • 48 results • page 1 of 5 • next >
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CNV detection using beakdancer and SVDetect
... hi i have whole genome of a mmalian in paired end aligned on reference genome using BWA. i used breakdancer to CNV detection but i do not know how interpret the results. where are CNVs in output?? also i used SVDetect cnv but it is hard to interpret too. manual of programs are not rich. anybody ...
svdetect breakdancer cnv written 6 weeks ago by kk.mahsa50 • updated 5 weeks ago by d-cameron1.0k
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bgzf_read error during samtools run
... hi when i used following command on my bam file: samtools view -F 4 myfile.bam | perl -lane 'print "$F[2]\t$F[3]"' > myfile.hits i got this message: [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [main_samview] truncated file. anybody can help me to resolve it. ...
software error cnv-seq samtools bgzf written 6 weeks ago by kk.mahsa50 • updated 6 weeks ago by Devon Ryan74k
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visualization of identified SSRs
... hi i used MISA (MIcroSAtellite identification tool) to SSRs of whole genome. Now i want to visualize my output, How can i do it? any program or package do it? ...
ssr visualize written 8 weeks ago by kk.mahsa50 • updated 7 weeks ago by Farbod3.0k
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SRA submission problem
... i tried to upload 59.5G SRA data to NCBI by Aspera connect using "I will upload all the files now via HTTP/Aspera" in SRA submission wizard, but due to slow internet, uploading stopped and a got an error that i must try again, I resumed Aspera connect and finally uploading done successfully. But whe ...
ncbi sra aspera connect written 9 weeks ago by kk.mahsa50
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Comment: C: how can i inter into my root directory in SRA (NCBI) and create subdirectory?
... i found my answer and share it with you using -d (Create target directory if it doesn't already exist) option and adding your desired name for sub-directory, your problem will be solved like this. ascp -i /home/genome/Gb/aspera.openssh \ -QT -l100m -k1 -d /home/genome/Gb/mySRA.gz \ ...
written 10 weeks ago by kk.mahsa50 • updated 10 weeks ago by Ram13k
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how can i inter into my root directory in SRA (NCBI) and create subdirectory?
... i want to submit my SRA in NCBI and using ascp and following command, my data uploaded in my root directory. ascp -i /home/genome/Gb/aspera.openssh -QT -l100m -k1 -d /home/genome/Gb/mySRA.gz subasp@upload.ncbi.nlm.nih.gov:uploads/xxxxxxxx@gmail.com_xxxxxx now, as NCBI's guide: I uploaded all ...
ncbi sra written 10 weeks ago by kk.mahsa50 • updated 10 weeks ago by Ram13k
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Comment: C: combine two fastq file (paired end) to submit in NCBI
... thanks genomax for your kindly advises ...
written 11 weeks ago by kk.mahsa50
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Comment: C: combine two fastq file (paired end) to submit in NCBI
... is it possible that file be harmed due to renaming? ...
written 11 weeks ago by kk.mahsa50
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Comment: A: dividing fastq file into 2 separate files
... you can use SRAtoolkit to do that ...
written 11 weeks ago by kk.mahsa50
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Comment: C: combine two fastq file (paired end) to submit in NCBI
... i renamed it by adding .fastq my files are in fastq format (four line per read) but in their name there is not .fq or .fastq so i renamed it and added .fastq then run reformat.sh on them and got above problem. i gathered my files via cat command successfully, can i submit output of cat command int ...
written 11 weeks ago by kk.mahsa50

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