User: nbhardwaj

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nbhardwaj100
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Posts by nbhardwaj

<prev • 45 results • page 1 of 5 • next >
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Comment: A: GATK HC not calling variants at the edges after clipping probes
... Just to let you all know that using Unified Genotyper called the variants that HC missed. So using UG now. ...
written 7 months ago by nbhardwaj100
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Comment: C: Remove hundreds of probes
... hi genomax, yes, that worked. What does `k=13` mean? Also, the reason why I had `minmerfraction=1.0` is because I wanted to remove only those 5' parts that were 100% identical to the probe sequences. I hope that it still does that. Yes, the probe sequences are in multi-fasta format. Thanks! ...
written 9 months ago by nbhardwaj100
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Comment: C: Remove hundreds of probes
... Hi chen, actually, it does work - I loaded it in a browser and it looked good. Thanks for the suggestion! ...
written 9 months ago by nbhardwaj100
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GATK HC not calling variants at the edges after clipping probes
... Hi, I am facing a strange issue with GATK 3.4. I have a set of PE fastq files. I first ran the variant calling pipeline using the following steps: bwa mem --> sam to bam --> mark duplicates using picard --> RealignerTargetCreator GATK 3.4 --> IndelRealigner --> HaplotypeCaller --> ...
gatk sequencing written 9 months ago by nbhardwaj100
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Comment: C: Remove hundreds of probes
... Thanks, genomax. I did try `bbduk.sh` but it did not give me what I expected. I ran it to only look for probes on the 5' end with exact matches in the first 31 bp as follows: bbduk.sh in1=L001_R1_001.fastq.gz in2=L001_R2_001.fastq.gz out1=bbmap_R1.fastq.gz out2=bbmap_R2.fastq.gz ref=RC_DLSO_and_UL ...
written 9 months ago by nbhardwaj100
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Comment: C: Remove hundreds of probes
... Hi Chen, I do have the sequences of the probes but I still tried it nonetheless - it worked but it did not remove all the probes (only about half of them were removed). I think its because it does not have all the info (the exact sequences of all the probes). ...
written 9 months ago by nbhardwaj100
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Remove hundreds of probes
... Hi, I have paired-end fastq file which contain the sequences of the target regions along with probes sequences on either side (in entirety or partially). I have sequences of all the 3,200 probes. I want to quickly trim the probe sequences from the fastq files if they occur on either side of the targ ...
probes trimming written 9 months ago by nbhardwaj100 • updated 9 months ago by chen1.7k
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Comment: C: demultiplexing Illumina output with fastq_multx
... I actually could not solve the problem. If you find the solution, please let me know too. I ended up using the de-multiplexing performed by the MiSeq Reporter itself such that MiSeq directly wrote individual FASTQ files. ...
written 10 months ago by nbhardwaj100
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Comment: C: picard tools HsMetrics not using duplicate reads to calculate coverage
... Pierre, sorry, I did not follow you; you suggest mapq==0 as a switch in HsMetrics? BTW, are there any other tools out there that can do the same: provide depth information on the intervals (supplied in a bed format) and some other post-alignment quality metrics? Thanks! ...
written 2.3 years ago by nbhardwaj100
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Comment: C: picard tools HsMetrics not using duplicate reads to calculate coverage
... Thanks, Pierre. I can try that. However, as I mentioned above that running HsMetrics on the sorted bam file which has not undergone duplicate marking gives the same results: Lower depth than actual due to duplicate reads. So, apparently, HsMetrics does not take duplicate reads into account even at t ...
written 2.3 years ago by nbhardwaj100

Latest awards to nbhardwaj

Popular Question 8 months ago, created a question with more than 1,000 views. For picard tools HsMetrics not using duplicate reads to calculate coverage
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Individual or population level variant calling?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For number of .bam reads mapping to genes in gff format
Popular Question 2.1 years ago, created a question with more than 1,000 views. For cuffmerge does not give merged.gtf
Popular Question 2.1 years ago, created a question with more than 1,000 views. For difference between BWA mem, sampe and bwasw
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Picard MarkDuplicates error: Value was put into PairInfoMap more than once
Popular Question 2.1 years ago, created a question with more than 1,000 views. For importance of known sites/resources in GATK pipeline
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Known SNPs for rice for Base recalibration using GATK
Popular Question 2.2 years ago, created a question with more than 1,000 views. For cuffmerge does not give merged.gtf
Popular Question 2.4 years ago, created a question with more than 1,000 views. For cuffmerge does not give merged.gtf

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