User: siyavash_damdar

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Posts by siyavash_damdar

<prev • 26 results • page 1 of 3 • next >
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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_damdar20
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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_damdar20
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mapping form different lane
... Hi to all I have 4 lanes (whole genome seq) from 1 sample, I want to know how can I mapping these sequence? ...
ngs bwa written 8 hours ago by siyavash_damdar20 • updated 7 hours ago by swbarnes23.4k
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Comment: C: WARN in GATK HaplotypeCaller
... thank you so much, Mr.Ram. ...
written 22 days ago by siyavash_damdar20
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WARN in GATK HaplotypeCaller
... 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 : ...
haplotypecaller gatk snp written 23 days ago by siyavash_damdar20 • updated 23 days ago by Ram14k
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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_damdar20
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Number of threads in BWA
... 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. ...
ngs alignment bwa written 29 days ago by siyavash_damdar20 • updated 28 days ago by d-cameron1.5k
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a question about HaplotypeCaller and skipping "indel realignment" and re-calibration" steps
... Hi can I skip "indel realignment" and re-calibration" steps, when I am using HaplotypeCaller ? ...
gatk snp gvcf written 4 weeks ago by siyavash_damdar20 • updated 4 weeks ago by Devon Ryan78k
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Comment: C: I want to know is it a true method ?
... I would recommend to sort the file by coordinates: which software can do it? ...
written 5 weeks ago by siyavash_damdar20
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Comment: C: I want to know is it a true method ?
... thank you so much for useful guidance. ...
written 5 weeks ago by siyavash_damdar20

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