User: oriolebaltimore

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Posts by oriolebaltimore

<prev • 34 results • page 1 of 4 • next >
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Answer: A: htseq-counts output merge into one matrix ??
... Is it considered best practice to sum up reads across replicates or to run HTSeq on merged BAM File after ccombing fastqs. Thanks Adrian ...
written 8 days ago by oriolebaltimore60
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When to remove duplicates using deduplication in Exome-Seq
... Hello group, To remove bias in calculating variant frequencies, we tend to remove PCR optical duplicates in Illumina exome-Seq protocols. However, in targeted sequencing, we do not remove PCR duplicates. I am not sure about Illumina truseq rapid exome sequencing library approach. Should the BAM ...
trueseq dna-seq exome-seq truseq gatk written 4 weeks ago by oriolebaltimore60 • updated 4 weeks ago by Charles Warden6.1k
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Comment: A: Bigwig format and operation
... I also responded to another similar post and requested the same question in the same forum. I apologize if that violates duplicate question rules. ...
written 8 weeks ago by oriolebaltimore60
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Comment: C: Bigwig format and operation
... Perfect. Got it!! Thanks ATpoint. ...
written 8 weeks ago by oriolebaltimore60
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Comment: A: bigWig to bed for regions above/below threshold
... Dear Alex and Sean, could you please help understand what is the threshold value mean in either ATAC-Seq or ChIP-Seq in wig file obtained after bigWigToWig conversion. Particularly, in bedgraph format what is the 4th column in dataValue and what are the norms for selecting the threshold. Thanks Ad ...
written 8 weeks ago by oriolebaltimore60
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Comment: C: Bigwig format and operation
... Thanks. I added them purposefully for formatting purpose as I felt this is not code and saw no other formatting option for the sample lines from wig file. Thanks. ...
written 8 weeks ago by oriolebaltimore60
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Bigwig format and operation
... Dear users, I read through UCSC wiggle format (BigWig) in depth. I understand the format about variable step, fixed step and use of bigwig to visualize in a browser etc. However, I don't have clarity on using ChIP-Seq, ATAC-Seq data in bigWig format. > Example of the Wig file after converting ...
bigwig chip-seq atac-seq written 8 weeks ago by oriolebaltimore60
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Comment: A: How to fix .bam file that was diagnosed as "MISSING_READ_GROUP" by Picard Valida
... Hi Pierre and other experts, I used Picard ValidateSamFile and found the following errors. about mate not found and missing read group. I used tophat instead of BWA. Is there any difference between Tophat and BWA derived BAM files. Also what to do abut Mate not found in a PE reads. It should ...
written 4 months ago by oriolebaltimore60 • updated 4 months ago by genomax62k
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Answer: A: Identify reads that span intron-exon junctions in RNA-Seq
... Dear Alex, Thank you so much. worked beautifully!! Adrian ...
written 5 months ago by oriolebaltimore60
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TCGA data on cloud
... Dear group, I apologize if I am asking a question that has been discussed here. I could not find a related search to my question. I am interested in running analyses on TCGA raw data on cloud that hosts raw data already. I have necessary permissions to access raw TCGA data. What I am looking int ...
cloud computing tcga rna-seq written 5 months ago by oriolebaltimore60 • updated 5 months ago by krithika.gu250

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Popular Question 20 months ago, created a question with more than 1,000 views. For RNA-Seq raw fastq files from TCGA

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