User: rohitsatyam102
rohitsatyam102 • 60
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Posts by rohitsatyam102
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... Hi All!!
I have searched a lot on how to fetch the subtelomeric region sequences chromosome wise. However I am unable to do that. Does someone have some experience doing that. I referred to this paper Mapping and Initial Analysis of Human Subtelomeric Sequence Assemblies
https://www.ncbi.nlm.nih.go ...
written 1 day ago by
rohitsatyam102 • 60
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Comment:
C: Sorting the BEd File
... Hi @Pierre
I found my mistake just now. I was using 2 in place of 2n. And that made all the difference. ...
written 8 days ago by
rohitsatyam102 • 60
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... Hi all
I was trying to sort BED file using the following command
sort -k1,1 -k2,2n in.bed > in.sorted.bed
The description of bedtools closest [here][1] says
> bedtools closest requires that all input files are presorted data by chromosome and then by start position
However I am getting th ...
written 8 days ago by
rohitsatyam102 • 60
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Comment:
C: TSS file for hg19
... This post can guide you: https://randomstate.net/2018-06-28-getting-refseq-gene-tss-from-ucsc/ ...
written 9 days ago by
rohitsatyam102 • 60
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... Hi all!
I am trying to understand the following regular expression.
![enter image description here][1]
In the above figure the author have used regular expression to identify G4 motifs in greedy and non-greedy fashion.
- Non-overlapping Greedy (?:(G{3}[ATGC]{1,7}){3}G{3})
- Non-overlapping No ...
written 15 days ago by
rohitsatyam102 • 60
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... I agree with you @Eric.
I always get data in gzip format. It really a tiring process to uncompress it and recompress it using fqz_comp to .fqz files. Moreover these new file formats aren't software friendly as gz and required to be decompressed into bigger fastq file such as during fastqc fastqc &l ...
written 23 days ago by
rohitsatyam102 • 60
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... The Depth of Coverage is depreciated in GATK4. It's only available in GATK3. See [here][1]
[1]: https://gatkforums.broadinstitute.org/gatk/discussion/11535/depth-of-coverage-in-gatk-4#latest ...
written 26 days ago by
rohitsatyam102 • 60
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... I tried using QualiMap2 on HPC. It just doesn't work. ...
written 26 days ago by
rohitsatyam102 • 60
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... I used picard to mark duplicates to further substantiate my suspicion and confirmed that maximum of the reads (above 90%) were duplicates. My further strategy is to separate the duplicates and unique reads and visualise in IGV which region are these actually. ...
written 4 weeks ago by
rohitsatyam102 • 60
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... Hi all!
> - HTK4ME1-1_S2_sorted
- 134765384 + 0 in total (QC-passed reads + QC-failed reads)
- 0 + 0 secondary
- 0 + 0 supplementary
- 0 + 0 duplicates
- 134765384 + 0 mapped (100.00%:N/A)
- 134765384 + 0 paired in sequencing
- 67386044 + 0 read1
- 67379340 + 0 read2
- 34355482 + 0 pr ...
written 4 weeks ago by
rohitsatyam102 • 60
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