User: soleimani_homa
soleimani_homa • 0
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Posts by soleimani_homa
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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_homa • 0
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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_homa • 0
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... 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 ...
written 14 days ago by
soleimani_homa • 0
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C: losing reads bam to fastq
... OK,Thanks very much for you patient explain.
...
written 4 months ago by
soleimani_homa • 0
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C: losing reads bam to fastq
... Thanks a lot for you kind help. ...
written 4 months ago by
soleimani_homa • 0
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... 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 ...
written 4 months ago by
soleimani_homa • 0
• updated
4 months ago by
finswimmer ♦ 11k
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... 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!
...
written 5 months ago by
soleimani_homa • 0
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...
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_homa • 0
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... 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 ...
written 7 months ago by
soleimani_homa • 0
• updated
7 months ago by
WouterDeCoster ♦ 39k
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