User: whaiyu06

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whaiyu0620
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9 months, 1 week ago
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2 years, 6 months ago
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Posts by whaiyu06

<prev • 15 results • page 1 of 2 • next >
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Comment: C: GATK IndelRealigner make mistakes
... I solved this issue by adding another parameter -filterNoBases. Thanks for your advice. ...
written 9 months ago by whaiyu0620
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Comment: C: GATK IndelRealigner make mistakes
... Thanks.There nothing output as your command. ...
written 10 months ago by whaiyu0620
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GATK IndelRealigner make mistakes
... hello, I used the command to realignment around indels.The command as follows: java -jar /Software/GenomeAnalysisTK-3.6/GenomeAnalysisTK.jar \ -R $ref \ -T IndelRealigner \ -targetIntervals A01-2m-B8_merge.mark.intervals \ -I A01-2m-B8_merge.mark.bam \ -o A01-2m-B8_merge ...
alignment sequencing written 10 months ago by whaiyu0620 • updated 10 months ago by Pierre Lindenbaum115k
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Picard MarkDuplicates /SAM validation error
... Hello,everyone I used Picardtools/MarkDuplicates as following: java -jar picard.jar \ INPUT=A01-2m-D6.sort.bam \ OUTPUT=A01-2m-D6.bam \ METRICS_FILE=A01-2m-D6.metrics CREATE_INDEX=true 2>A01-2m-D6.picard_MarkDuplicates.stderr then I met thus error: picard.sam.mar ...
alignment sequencing written 10 months ago by whaiyu0620 • updated 10 months ago by Pierre Lindenbaum115k
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Comment: C: Error while running BWA mem
... I met the same issue as you.So how do you deal with this error?It is the memory no enough to compute or the reference is not complete or any other reason?Thanks ! ...
written 10 months ago by whaiyu0620
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Comment: C: bwa mem mapping
... Yes,I have checked them ,but there's nothing wrong have been reported. ...
written 10 months ago by whaiyu0620
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Comment: C: bwa mem mapping
... I used 32 threads ,8 cpu cores of the Linux server to map the reads.I don't know the other config of the machine ,but if it is necessary I'll check them.Thank you! ...
written 10 months ago by whaiyu0620
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Comment: C: bwa mem mapping
... the command line I used is:`nohup bwa mem -t 4 -M -R "@RG\tID:A01-2m-B8\tSM:A01-2m-B8\tPL:illumina\tLB:lib1\tPU:unit1" /public1/data/reference/public/Homo_sapiens_assembly19.fasta /public1/barcode/WGS_SC/PF_data/SingleCellAnal/trimmed.A01-2m-B8_R1.fastq.gz /public1/barcode/WGS_SC/PF_data/SingleCellA ...
written 10 months ago by whaiyu0620 • updated 10 months ago by genomax59k
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bwa mem mapping multi-thread/single thread
... Hi everyone : I used the software cutadapt to remove the adapter after I received the raw data from sequencing company.(The command is: cutadapt \ -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC \ -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT \ ...
alignment sequencing written 10 months ago by whaiyu0620 • updated 10 months ago by genomax59k
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Comment: C: How to map reads to tiny reference using bowtie2
... Thanks for your reply.It is not appropriate for bowtie2 to align the longer reads to short ref. I have used blast to search the aligned sequences,but don't consider the quality of sequences in this way. Furthermore,I don't understand how to operate the second strategy, you means it is also don't t ...
written 19 months ago by whaiyu0620

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