User: kk.mahsa

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kk.mahsa100
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Posts by kk.mahsa

<prev • 52 results • page 1 of 6 • next >
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(Closed) remove space between columns
... hi i have a vcf file containing 4 columns like below. NW_012.1 35 A G now i want remove space between columns and output will be as below NW_012.135AG how can do this? ...
snp awk written 24 days ago by kk.mahsa100
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diffrence between number of reads in fastqc reports and collectalignmentsummarymetrics of Picard
... hi everyone i have 4 fastq files (two lane correspond to one organism), after filtration of reads, FastQC tell me that total number of reads is 628748302, i mapped them to reference genome and merged resulted two bam file and then sorted it. Now when i run collectalignmentsummarymetrics of Picard t ...
reads picard bam fastqc written 11 weeks ago by kk.mahsa100
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Comment: C: how to get common variants between two species?
... thanks but this is not what i want ...
written 13 months ago by kk.mahsa100
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how to get common variants between two species?
... i have sequencing data for two species, that they are able to mate together. now i want to extract common variants between them. To do this, must i map two data set in one reference genome or there are other ways? thanks in advance ...
next-gen snp common variant written 13 months ago by kk.mahsa100 • updated 13 months ago by tiago2112871.1k
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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 14 months ago by kk.mahsa100 • updated 14 months ago by d-cameron2.0k
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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 14 months ago by kk.mahsa100 • updated 14 months ago by Devon Ryan88k
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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 15 months ago by kk.mahsa100 • updated 15 months ago by Farbod3.2k
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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 15 months ago by kk.mahsa100
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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 15 months ago by kk.mahsa100 • updated 15 months ago by RamRS20k
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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 15 months ago by kk.mahsa100 • updated 15 months ago by RamRS20k

Latest awards to kk.mahsa

Popular Question 11 months ago, created a question with more than 1,000 views. For how can i remove duplicated variants from vcf file?
Popular Question 11 months ago, created a question with more than 1,000 views. For converting lowercase letters to uppercase letters in fasta file

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