User: Kssr

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Kssr110
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Posts by Kssr

<prev • 31 results • page 1 of 4 • next >
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disabling duplicate read filter -Mutect 1.1.4
... I would like to disable duplicate read filter using -drf DuplicateRead with Mutect v1 for a targeted sequencing project. Looks like disabling the read filter option is not available with Mutect v1 as it runs with GATK v2.2 is there a better way to solve this apart from unmarking the BAM's? ...
gatk mutect written 3.2 years ago by Kssr110
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Comment: C: picard CalculateHSMetrics error
... I understand the error is about sequence dictionaries. Yes, my files -bam and target & probe intervals have .dict indexes. I'm not sure what the error message implies, @SQ lines in the header of files are same. Only difference is my bam has GO:none in the @HD line and @PG lines(which I think is ...
written 3.6 years ago by Kssr110
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picard CalculateHSMetrics error
... I'm trying to run picard CalculateHSMetrics step on a bam file to get hybrid selection metrics and per target coverage across a list of target and probe intervals. I get the below error, SequenceUtil$SequenceListsDifferException: Sequence dictionaries are not the same size (87, 85) I checked ...
picard metrics written 3.6 years ago by Kssr110 • updated 3.6 years ago by mastal5112.0k
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Answer: C: Malformed SAM line error with HTSeq
... I ran the step below to keep only alignments mapped in proper pair and ran HTSeq, it runs fine now without any errors. Looks like the malformed SAM line was filtered out in the process. samtools view -h -f 0x2 nameSrt.fixmate.bam ...
written 3.7 years ago by Kssr110 • updated 14 months ago by RamRS24k
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Malformed SAM line error with HTSeq
... I'm running HTSeq to get counts on a sam file following the below steps, samtools sort -n tmp.bam nameSrt samtools fixmate nameSrt.bam nameSrt.fixmate.bam samtools view -h nameSrt.fixmate.bam >nameSrt.fixmate.sam python -m HTSeq.scripts.count -f sam -r name -s $ss_library -a 10 ...
htseq-count written 3.7 years ago by Kssr110 • updated 14 months ago by RamRS24k
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editing count.py script of HTSeq to work with bed file
... I have a bed file with peaks called on chipseq data with each line in the format, 1 15520461 15520630 samplex_peak_1 I want to count reads across the peaks called using htseq count. I am new to using HTSeq count, I have installed the package and I'm trying to edit the count.py script. I came acr ...
htseq bed written 3.9 years ago by Kssr110 • updated 3.9 years ago by sunhanice220
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Comment: C: Looking for opinions on PhD programs in Genetics and Genomics/Bioinformatics
... I agree with your opinion. I just wanted to get an overview of these programs/other programs. I'll look in to the research interests of faculty at respective institutes and network more. Thanks!  ...
written 5.0 years ago by Kssr110
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Comment: C: Looking for opinions on PhD programs in Genetics and Genomics/Bioinformatics
... Thank you for your thoughtful comments and suggestions. ...
written 5.0 years ago by Kssr110
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Forum: Looking for opinions on PhD programs in Genetics and Genomics/Bioinformatics
... Hello all, I have research experience working as a Bioinformatics programmer/analyst for close to 3 years post my Masters in Bioinformatics from USA. I have experience working with Next Gen Sequencing data sets from different platforms and technologies. I wish to apply for PhD programs in Genetics ...
forum phd genomics written 5.0 years ago by Kssr110 • updated 5.0 years ago by Dan D6.9k
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Answer: A: Errors While Running Printreads Walker Of Gatk
... I ran Picard's FixMateInformation step, and revalidated my BAM. However, I still get the following error: Mate not found for paired read. Any ideas on how to fix this? ...
written 6.1 years ago by Kssr110

Latest awards to Kssr

Great Question 3.6 years ago, created a question with more than 5,000 views. For Samtools Rmdup And Picard Mark Duplicates
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Errors While Running Printreads Walker Of Gatk
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Quality Scores In A Multi Sample Vcf File
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Quality Scores In A Multi Sample Vcf File
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Quality Scores In A Multi Sample Vcf File
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Filtering Variant Calls Based On Genotype Quality
Popular Question 6.0 years ago, created a question with more than 1,000 views. For Which Aligner Should I Use For Mapping Bacterial Rna-Seq Data
Popular Question 6.0 years ago, created a question with more than 1,000 views. For Samtools Rmdup And Picard Mark Duplicates
Popular Question 6.0 years ago, created a question with more than 1,000 views. For Mpileup On Merged .Bam File
Popular Question 6.0 years ago, created a question with more than 1,000 views. For Filtering Variant Calls Based On Genotype Quality
Student 6.0 years ago, asked a question with at least 3 up-votes. For Which Aligner Should I Use For Mapping Bacterial Rna-Seq Data

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