User: soleimani_homa

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Posts by soleimani_homa

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Comment: A: depth of coverage - ANOVA - R
... Since ANOVA is run in each row for each position of genome between breeds, and the number of positions are around 900,000, I can't plot them, so I want to know is it necessary checking the normality? How can I do that? If Shapiro Test is over-sensitive what procedure is recommended? Thank you for yo ...
written 12 days ago by soleimani_homa0
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Comment: C: depth of coverage - ANOVA - R
... Hi Kevin Blighe, thanks for the reply. I have 115 samples totally, each breed has 20 or 25 samples. Before doing ANOVA should I do a normality test (Shapiro test) or dip test or a non-parametric ANOVA (Kruskal-Wallis test)? Which one is better? At first I did the dip test, but most of the positions ...
written 12 days ago by soleimani_homa0
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depth of coverage - ANOVA - R
... Hello, I'm analyzing output of depth of coverage between five breeds. I want to understand where the depth of coverage of genome has changed between five breeds. I have 5 files containing positions in the rows and samples of each breeds in the columns. then I joint them . Now I want to perform an A ...
R depth of coverage anova written 14 days ago by soleimani_homa0
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Comment: C: losing reads bam to fastq
... OK,Thanks very much for you patient explain. ...
written 4 months ago by soleimani_homa0
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Comment: C: losing reads bam to fastq
... Thanks a lot for you kind help. ...
written 4 months ago by soleimani_homa0
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losing reads bam to fastq
... Hi all, I am trying to realign a whole genome BAM file from one reference genome to another. Because the reference genome is updated. The process involves converting the name-sorted BAM file to fastq, then realigning the fastq to a new reference. 1. `samtools sort -n input.bam -o input_n.sorted.bam ...
fixmate fastq bam whole genome sequencing written 4 months ago by soleimani_homa0 • updated 4 months ago by finswimmer11k
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(Closed) How to extract fasta sequence from BAM files generated using BWA
... Hi everyone, I need to convert a BAM to a FASTA. BAM file generated by BW aligner. I need forward and reverse sequences separately in fasta format. I appreciate any of your solutions. Thanks a lot! ...
fasta alignment bam sequencing written 5 months ago by soleimani_homa0
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Comment: C: best way to separate copy number variations from VCF files
... Thanks a lot for the reply Since my VCF files are derived from the GATK software, I would prefer to continue the path with the GATK. Do you have any suggestions for separating the CNVs from the VCF file using GATK? ...
written 6 months ago by soleimani_homa0
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best way to separate copy number variations from VCF files
... Hi I am interested in finding copy number variation in my samples. I have raw VCF files. I have looked at the previous questions, but I have not gotten one clear answer. Is there a walker to find CNV's (duplications or deletions) in GATK from raw VCF files? Hope to hear from you soon. Regards Hom ...
snp cnvs written 7 months ago by soleimani_homa0 • updated 7 months ago by WouterDeCoster39k

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