User: nbhardwaj

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nbhardwaj80
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Posts by nbhardwaj

<prev • 38 results • page 1 of 4 • next >
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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 days ago by nbhardwaj80
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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 17 months ago by nbhardwaj80
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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 17 months ago by nbhardwaj80
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Comment: C: picard tools HsMetrics not using duplicate reads to calculate coverage
... Yes, sorry, I meant depth. HsMetrics is reporting a mean depth of 2X in regions where I can see from the bam file in IGV that there are 30 reads mapping in that location. Please advise. ...
written 17 months ago by nbhardwaj80
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picard tools HsMetrics not using duplicate reads to calculate coverage
... Hi, I am using Picard CollectHsMetrics tool to obtain a bunch of statistics about the regions in my targeted panel such as mean coverage and mean coverage for each interval. Since the panel is small, there is a huge number of duplicate reads and CollectHsMetrics only takes into account the unique re ...
duplicates picard hsmetrics written 17 months ago by nbhardwaj80 • updated 17 months ago by Pierre Lindenbaum99k
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Comment: C: Similarity between two sets of paired-end fastq files
... I thought that by comparing the fastq files I can rule out any effect of the downstream steps (QC, alignment, VC etc) which are different between the two sets can really narrow down the problem up to the sequencing steps. Thanks! ...
written 19 months ago by nbhardwaj80
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Comment: C: Similarity between two sets of paired-end fastq files
... I thought that comparing the fastq files will really narrow down the problem up to the sequencing steps (with out any downstream step having any effect). But I can compare the bams as well. Thanks! ...
written 19 months ago by nbhardwaj80
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Similarity between two sets of paired-end fastq files
... Hi, Is there a tool out there which will allow me, in any way, to determine how similar two fastq file sets (paired-end) are? It could be any metric like number of identical reads etc. or any other metric which can be relevant in this case. I need this to diagnose the reason behind low agreement of ...
fastq paired-end rna-seq written 19 months ago by nbhardwaj80 • updated 19 months ago by apelin20460
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Comment: C: QC tool for targeted gene panel (like FastQC for WGS)
... I was looking for something to analyze FASTQs as well. Would you have a suggestion? For post-alignment, Charles mentioned HsMetrics from Picard below. ...
written 19 months ago by nbhardwaj80
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Comment: C: QC tool for targeted gene panel (like FastQC for WGS)
... Thanks Charles! One quick question that I could not clarify upon skimming through the description: What is the difference between Bait and Target region? Should they both be input in a .bed format? Thanks again! ...
written 19 months ago by nbhardwaj80

Latest awards to nbhardwaj

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