User: shopnil99

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shopnil990
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Posts by shopnil99

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Error while running normOffsets in diffhic
... thank you for the explanation Aaron. ...
written 13 days ago by shopnil990
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Comment: C: Error while running normOffsets in diffhic
... Thank you! changing type = "loess" to method="loess" worked out really well. ...
written 13 days ago by shopnil990
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Error while running normOffsets in diffhic
... I ran the following code to create and filter my "data" object: data <- squareCounts(input, hg19.param, width=bin.size, filter=1) keep <- aveLogCPM(asDGEList(data)) > 0 data <- data[keep,] When I tried normalizing the filtered data using the following command I get the error below d ...
csaw diffhic written 15 days ago by shopnil990 • updated 15 days ago by Aaron Lun24k
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Comment: C: rotPlaid error "Error in if (x.min >= x.max) { : missing value where TRUE/FALSE
... Thank you for your answer Aaron. Indeed, using the fragment output from HICUP Digester to create the param object leads to missing "seqlenghts" and eventually the above error. I used the devtools package in R/3.6.0 to turn on dev_mode and was able to use cutGenome for multiple restriction sites, whi ...
written 26 days ago by shopnil990
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rotPlaid error "Error in if (x.min >= x.max) { : missing value where TRUE/FALSE needed"
... I am following chapter 8 of the user guide to detect differential domain boundaries. My analysis pipeline is as follows: I used the HICUP digester script to generate the restriction digest file for the Arima restriction enzyme cocktail and used this file to generate the hg19_param file. I mappe ...
diffhic rotplaid written 27 days ago by shopnil990 • updated 27 days ago by Aaron Lun24k
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Comment: C: diffHic presplit_map.py --sig option for HiC libraries prepared with restriction
... Thank you for the explanation Aaron. I went looking for the Hic-Pro pipeline you mentioned and I found a mapping pipeline from Arima at https://github.com/ArimaGenomics/mapping_pipeline. This creates a combined bam file from paired end reads and Marks duplicates using Picard tools. Do you think this ...
written 4 weeks ago by shopnil990
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diffHic presplit_map.py --sig option for HiC libraries prepared with restriction enzyme cocktail from Arima genomics
... Hi, I prepared some of my Hi-C libraries with the Arima Genomics Hi-C prep kit that uses a restriction enzyme cocktail. If anyone works with similar libraries, do you know what option I should use for --sig when running presplit_map.py to produce bam files. thanks, - Iftekhar ...
diffhic arima genomics presplit_map.py written 4 weeks ago by shopnil990 • updated 4 weeks ago by Aaron Lun24k
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Answer: A: diffHic presplit_map.py pysam.SamtoolsError
... I originally got this error message while running presplit_map.py using python-2.7.10 (with pysam 0.8.4), cutadapt-1.8.3 and bowtie2-2.2.4 [E::hts_open] fail to open file './tmpnA4PdG/sorted.bam' Traceback (most recent call last): File "presplit_map.py", line 242, in pysam.sort("-o", bsorte ...
written 5 weeks ago by shopnil990
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Comment: C: diffHic presplit_map.py pysam.SamtoolsError
... Hi Aaron, The Bam file HIC003_R1.fastq.bam looks ok: M00336:181:000000000-A29H6:1:1101:17139:1645 2129 chr17 62341747 42 80M20H * 0 0 HGFHHGCFDAGBHGG2HGFHHHFFHFHGFACGGFFDGGHHHHHHHGHHFGG AS:i:-8 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:0A50C2 M00336:181:000 ...
written 5 weeks ago by shopnil990
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diffHic presplit_map.py pysam.SamtoolsError
... Hi, I am running the presplit_map.py script on a SLURM cluster on a small dataset (MboI restriction enzyme used). here's the command I am running: ``` python presplit_map.py -G ~/../Bowtie2Index/hg19 -1 ~/../fastq/HIC003_R1.fastq.gz -2 ~/../fastq/HIC003_R2.fastq.gz --sig GATCGATC -o HIC003.bam `` ...
diffhic pysam.samtoolserror pysam.sort written 5 weeks ago by shopnil990

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Scholar 5 weeks ago, created an answer that has been accepted. For A: diffHic presplit_map.py pysam.SamtoolsError

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