User: siyavash_damdar
siyavash_damdar • 20
- Reputation:
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- 3 months, 1 week ago
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Posts by siyavash_damdar
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Comment:
C: mapping form different lane
... I want for SNP discovery. so if I want to map all files in one step then I faced problems in GATK? is it true?
...
written 2 hours ago by
siyavash_damdar • 20
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Comment:
C: mapping form different lane
... No, I mean, I have 4 lanes that Each one included a forward and a reverse read so In total I have 8 fastq.gz files. I do not know how can I do mapping? because, BWA accept only two inputs ( a forward and a reverse read) not 8 inputs. ...
written 8 hours ago by
siyavash_damdar • 20
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... Hi to all
I have 4 lanes (whole genome seq) from 1 sample, I want to know how can I mapping these sequence? ...
written 8 hours ago by
siyavash_damdar • 20
• updated
7 hours ago by
swbarnes2 ♦ 3.4k
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Comment:
C: WARN in GATK HaplotypeCaller
... thank you so much, Mr.Ram. ...
written 22 days ago by
siyavash_damdar • 20
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... Hi to all
I ran this command:
java -Xmx16g -jar /mnt/unison/home/ymiar/siavash/GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar \
-R dna.toplevel.fa -T HaplotypeCaller -I samp1 -I samp2 -I samp3 \
-o tothap.raw.snps.indels.g.vcf
and after running I have many same this log : ...
written 23 days ago by
siyavash_damdar • 20
• updated
23 days ago by
Ram ♦ 14k
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Comment:
C: Number of threads in BWA
... Thank you so much. I mean if once I run bwa with 6 threads and once again repeat this with 12 threads then I have different results(output)? ...
written 29 days ago by
siyavash_damdar • 20
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... Hi to all
I have a question about Number of threads in bwa. Does it (Number of threads) any effect on the final result? or only affect on analyzing time. ...
written 29 days ago by
siyavash_damdar • 20
• updated
28 days ago by
d-cameron • 1.5k
2
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... Hi
can I skip "indel realignment" and re-calibration" steps, when I am using HaplotypeCaller ? ...
written 4 weeks ago by
siyavash_damdar • 20
• updated
4 weeks ago by
Devon Ryan ♦ 78k
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... I would recommend to sort the file by coordinates: which software can do it? ...
written 5 weeks ago by
siyavash_damdar • 20
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... thank you so much for useful guidance. ...
written 5 weeks ago by
siyavash_damdar • 20
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