User: Diedes

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Diedes20
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Posts by Diedes

<prev • 9 results • page 1 of 1 • next >
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Forum: scRNA rising in popularity, what comes next?
... Now scRNA is getting very popular, just the way next generation sequencing became very popular over the last 15 years, I was wondering, what would be the next level of sequencing? What will be even deeper than things like scRNA, linked reads or long read sequencing? ...
future scrna forum written 7 weeks ago by Diedes20 • updated 7 weeks ago by dsull1.2k
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Comment: C: Is the upregulation of ribosome genes in scRNA-seq reliable?
... Hey, Sorry for the late reply, did not see you post earlier. I did see something very similar in data where they gated for only a subset of tcells. I made the assumption that this has to do with the fact the cells are very similar to the others on transcription level. This similarity causes that ri ...
written 7 weeks ago by Diedes20
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Comment: C: Reformat my txt file
... If you have this A b, c, d, e B f, g, h, Then `awk -F',| ' '{for (i=2;i 0){print $1,$i}}}' txt.txt` It even solves this: A b,c, d,e,f, g,h, i, o B h,d, y,u, i, o, C h f d,d g k l Or even if you have multiple spaces or comas between two letters, it will have the sam ...
written 8 weeks ago by Diedes20 • updated 8 weeks ago by RamRS27k
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Comment: C: CellRanger scRNA .mtx only uses 15% of reads in .bam?
... > I'd also expect some reads to be DNA contamination and to map to genomic regions not in any gene/transcript. Ah good point! So what I have been doing, is to write a script that would create a .mtx file out of a bam file, as I do not have the RAM capacity to go back to fastq and run celrange ...
written 8 weeks ago by Diedes20
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Comment: C: Run Cellranger Count with Novogene fastq files
... What is the output of `zcat DVC1_CKDL190145170-1a-SI_GA_A1_HTCTKDSXX_L4_* | head -n 8` ...
written 8 weeks ago by Diedes20
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Comment: C: CellRanger scRNA .mtx only uses 15% of reads in .bam?
... I also checked if the bam file contained many reads below a Q score of 30 and all reads I checked actually have higher than 30. (I believe 30 was the cutoff). Didnt check all due my code being slow. samtools view -h file.bam | awk '{if (substr($1,1,1) != "@" && $0 ~ /GN:Z:/){print}}' | ...
written 8 weeks ago by Diedes20
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Comment: C: CellRanger scRNA .mtx only uses 15% of reads in .bam?
... Hi, Thank you and all others for answering. It turns out that those 1/3rd that I did not get in my recreated matrix, are actually empty entries in the original CellRanger matrix. Basically the genes are not removed from features.tsv and the .mtx file is not adjusted. I think this happens after the ...
written 8 weeks ago by Diedes20
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Comment: C: CellRanger scRNA .mtx only uses 15% of reads in .bam?
... Hey, wouldn't those UMIs be corrected in the BAM? Althought I did just find out that my problem is probably that I did not correct for UMIs, so gonna rerun my script and give an update later. Thanks for your input! ...
written 8 weeks ago by Diedes20
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CellRanger scRNA .mtx only uses 15% of reads in .bam?
... Hi, For a few days I have been trying to convert .bam to .mtx. Which on its own is not that hard. The real problem is reproducing the results. I am using a bamfile which already has a .mtx file, so what I found was this. The bam file has nearly 245 million reads with a MAPQ value of 255 where the ...
.bam .mtx scrna cellranger single cell written 8 weeks ago by Diedes20 • updated 8 weeks ago by i.sudbery7.8k

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