User: rohitsatyam102

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Posts by rohitsatyam102

<prev • 28 results • page 1 of 3 • next >
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From where to get Sub-telomeric Region Coordinates/ sequences for each chromosome
... 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 ...
genome gene chip-seq assembly written 1 day ago by rohitsatyam10260
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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 rohitsatyam10260
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Sorting the BEd File
... 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 ...
genome gene next-gen written 8 days ago by rohitsatyam10260
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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 rohitsatyam10260
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Greedy-Non greedy Pattern search
... 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 ...
genome written 15 days ago by rohitsatyam10260
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Comment: C: Reliable Fastq compression programs
... 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 rohitsatyam10260
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Comment: C: Tools To Calculate Average Coverage For A Bam File?
... 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 rohitsatyam10260
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Comment: C: Tools To Calculate Average Coverage For A Bam File?
... I tried using QualiMap2 on HPC. It just doesn't work. ...
written 26 days ago by rohitsatyam10260
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Comment: C: MACS2 "total fragments in treatment" gives less number of fragments than expecte
... 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 rohitsatyam10260
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MACS2 "total fragments in treatment" gives less number of fragments than expected
... 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 ...
genome next-gen chip-seq written 4 weeks ago by rohitsatyam10260

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