User: akh22

gravatar for akh22
akh2240
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40
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New User
Location:
United States
Last seen:
1 week ago
Joined:
5 years, 11 months ago
Email:
a****@pitt.edu

Posts by akh22

<prev • 43 results • page 1 of 5 • next >
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Disappearing CB, the bam tag after samtools sort -t CB
... I've been trying to setup an analysis pipline for RNAvelocity in AWS EC2. I used one of the 10x dataset, **10k Peripheral blood mononuclear cells (PBMCs) from a healthy donor, Single Indexed**, as a test model to setup the pipeline. For speed and cost saving, I first used samtools to sort a 10P ...
samtools rna-seq sequencing written 10 days ago by akh2240
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Comment: C: empty fastq files created by docker bcl2fastq2 v2.20 OSX
... The input folder appears to be intact, containing everything original except the samplesheet.csv which I had to create based on a sample submission sheet. I think the issue may be incorrect samplesheet entries, or some corrupted files which will generate errors, but I dont se them. At this poin ...
written 4 weeks ago by akh2240
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Comment: C: empty fastq files created by docker bcl2fastq2 v2.20 OSX
... I modified the samplesheet.csv as follows; [Data] Lane Sample_ID Sample_Name Sample_Plate Sample_Well i7_Index_ID index i5_Index_ID index2 Sample_Project Description 1 PI0001 Sample_1 A01 D701 ATTACTCG D501 TATAGCCT Mouse 1 PI0002 Sample_2 B01 D701 ATTACTCG D502 ATAGAGG ...
written 5 weeks ago by akh2240
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Comment: C: empty fastq files created by docker bcl2fastq2 v2.20 OSX
... I wish I could use you script but the "Underdetermined" file is also 0K. Also, single reads were done with dual index. So the entry of the second index in the samplesheet is wrong in this case ? ...
written 5 weeks ago by akh2240
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Comment: C: empty fastq files created by docker bcl2fastq2 v2.20 OSX
... @genomax, It did generate all the fastqs for entires in the samplesheet.csv except one I don't know where this **Undetermined_S0_R1_001.fastq.gz** came from, which was not in the samplesheet.csv. I forgot to mention that these are single reads. Also, I did try run this without `--with-fai ...
written 5 weeks ago by akh2240 • updated 5 weeks ago by genomax91k
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empty fastq files created by docker bcl2fastq2 v2.20 OSX
... HI, I installed a following docker image, REPOSITORY TAG IMAGE ID CREATED SIZE zymoresearch/bcl2fastq latest 037f216c2523 13 months ago 117MB and run a following command; docker run -d --name bcl2fastq - ...
sequence assembly next-gen rna-seq written 5 weeks ago by akh2240
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Comment: C: Adjust for covariates
... Could you explain why residual rather than fitted value for adjusted value ? Residual is observed - fitted so adjusted value (covariate corrected) should be fitted ? ...
written 5 months ago by akh2240
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Amazon AWS setup for the bioinformatic analysis particularly scRNAseq
... I am trying to setup EC2 Amanzon AWS Rstudio and Linux AMI for scRNAseq analysis, and I am curios to see what sort of set up are sufficient and cost-effective for the bioinformatic use. For Rstuio, I tried the Rstudio AMI (developed by Louis Aslett )and mainly run **Seurat (integration), Single ...
aws rstudio scrnaseq written 6 months ago by akh2240 • updated 6 months ago by Kevin Blighe66k
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Comment: C: Getting a GTF of expressed repeat annotation from Ensembl
... Thanks. I think I got it. I followed the link you posted and the answer had the clue. It is included in a dan folder in the Fasta DNA dump. According to README, `dna` is unmasked DNA sequence and `dna-rm` corresponds to hand masked genomic DNA whereas `dan-sm` is the soft masked DNA sequence. I ...
written 6 months ago by akh2240
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Getting a GTF of expressed repeat annotation from Ensembl
... Hi, I can generate and download GTF of repeated sequence (mm10) from a USCD table browser by using a RepeatMasker track. Can anybody point me in the right direction to do this with Ensembl browser ? Also, Ensembl has a hand-made, (rather than using RepatMaskter) repeated sequence list ?, and i ...
sequence rna-seq written 6 months ago by akh2240

Latest awards to akh22

Popular Question 5 months ago, created a question with more than 1,000 views. For Loading 10x data into Monocle 3
Popular Question 6 months ago, created a question with more than 1,000 views. For A strategy to get Bacterial NCBI RefSeqs excluding contigs in an one file
Popular Question 12 months ago, created a question with more than 1,000 views. For Loading 10x data into Monocle 3
Popular Question 5.8 years ago, created a question with more than 1,000 views. For A strategy to get Bacterial NCBI RefSeqs excluding contigs in an one file

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