User: soleimani_homa
soleimani_homa • 0
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Posts by soleimani_homa
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... Hi every one
I have several genomic regions, when i search them in ensembl , I encounter such a page:
[chicken genome region][1]
What is differences between Gene Ensembl with different colour and part?
[1]: https://asia.ensembl.org/Gallus_gallus/Location/View?r=2%3A130986544-131255044 ...
written 3 months ago by
soleimani_homa • 0
• updated
3 months ago by
Emily_Ensembl ♦ 19k
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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 5 months 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 5 months 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 5 months ago by
soleimani_homa • 0
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C: losing reads bam to fastq
... OK,Thanks very much for you patient explain.
...
written 9 months ago by
soleimani_homa • 0
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C: losing reads bam to fastq
... Thanks a lot for you kind help. ...
written 9 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 9 months ago by
soleimani_homa • 0
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9 months ago by
finswimmer ♦ 12k
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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 10 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 11 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 11 months ago by
soleimani_homa • 0
• updated
11 months ago by
WouterDeCoster ♦ 41k
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