Peer Review? You mean offer a few Scientists a $100 million research grant to cover up the facts and save billions of dollars in lawsuits? After the last few years I’ve come to realise that peer reviewers are the HR department of Big Pharma
two observations: first, chatgpt gives me two entirely different sequences for forward (P7) and reverse (P5) primers. 2nd, my mac mini is way too slow to even install the software, let alone run it, so I'm doing it on Linux: `apt install sra-toolkit cutadapt bwa samtools igv`. maybe I'll write up a gist at github once I get it working, and will credit you if I do.
It seems that the rather mysterious author ( S.Chakraborty )of this bombshell publication has a lot of computer power and very much insight in these matters.I looked at some of his "published but not peer-reviewed" papers from 2020 and left very impressed.Sadly ,none of my highly respected collegues( specialists in genetics and vaccinology) whom I asked to comment on your as well as Ulrike Kämmerer et al. work, decided not to commentat all.
That's exactly what I was thinking when I was first trying to figure out how to download gzipped reads fast from SRA. (The answer is to use parallel-fastq-dump or ENA, because fastq-dump is slow and fasterq-dump doesn't support gzip.)
When I'm doing these tutorials, I tell people to download reads from ENA instead which doesn't require installing any additional utilities:
Oh my gosh - so much work (and hours) in this ‘solid resource with IT instructions’ article!! Thank you. Not only is this Substack post like a peer review (by renown Kevin McKernan) of a non peer-reviewed (but worthy of recognition) report (by Sandeep Chakraborty), but it’s affirmation of Sandeep’s collated written work - which by the way needs a date (2024) shown on page 1 or 13 on his report.
All this combined global work just helps towards the growing list from genome, virology and other experts, confirming high levels of DNA contamination being found in these novel but ‘bad’ and harmful C-19 jabs/shots.
P.S. This X post by ‘Fredy13’ on 11.12.2024 gives a Google doc of the list of “All current contamination papers linked”
I'm confused. After the first step, I have two fastq files, SRR18534011_1.fastq and SRR18534011_2.fastq.
They have lists of 120bp snippets, numbered identically in each file, but with entirely different bases. Eyeballing them, I'm pretty sure they're not the reverse reads of each other. What gives?
Thank you for this review, which I can almost understand. My computing abilities are not at a sufficient level to use your tutorial.
I do have a question, however. There are two types of Pfizer (and Moderna) mRNA vaxxes- the original PCR-produced trial shots, and the plasmid public injections. Has anyone been able to obtain or assess the original shots, or samples from the trial subjects, in order to analyse the residual modRNA and cDNA?
I wonder how many people in the world have the expertise to navigate let alone duplicate Kevin’s work? It’s apparent that regulators wouldn’t have this depth of special knowledge. It is obvious that Kevin has the stick-to-itiveness, the sign of a very curious and intelligent mind. Thank you.
Thats what we use. IDT lockdown probes that tile the whole plasmid. But we lose quantitive reads/million with this. RNA is a different beast. Lots of high copy transcripts you want to deplete. Just have to be careful when you do it.
For qualifying I would rather have QPCR. Maybe I am old school, but RNAseq is harder to quantify and it depends what you believe rather what it actually is.
No one wants to hear it, but for what it's worth...I believe in Jesus Christ's eminent return, to straighten back out the system of life He created so perfectly. By tampering, we can only do it harm. Does anyone believe that in heaven, tampering will be encouraged or needed?
Everything the "system" seeks after to enrich itself, is based on false science, which essentially are lies that obscure the truth. VERY few success stories can be told in this plethora of endeavors supposedly the "answer" to problematic issues.
I might change my view, if there EVER is shown to be REAL improvements made.
I'm confused, the paper isn't tracking mRNA from BNT162b2? It's looking at immune responses via RNA? I don't understand why this study is looked at in this context....?
Peer Review? You mean offer a few Scientists a $100 million research grant to cover up the facts and save billions of dollars in lawsuits? After the last few years I’ve come to realise that peer reviewers are the HR department of Big Pharma
Thank you for the detailed instructions! It's been over a decade since I did any bioinformatics work, and needed a refresher.
two observations: first, chatgpt gives me two entirely different sequences for forward (P7) and reverse (P5) primers. 2nd, my mac mini is way too slow to even install the software, let alone run it, so I'm doing it on Linux: `apt install sra-toolkit cutadapt bwa samtools igv`. maybe I'll write up a gist at github once I get it working, and will credit you if I do.
Wow. Impressive work and a great resource for those wanting to investigate further.
Every now and then I see use cases where ChatGPT can provide real value and cannot condemn the LLM field completely.
It seems that the rather mysterious author ( S.Chakraborty )of this bombshell publication has a lot of computer power and very much insight in these matters.I looked at some of his "published but not peer-reviewed" papers from 2020 and left very impressed.Sadly ,none of my highly respected collegues( specialists in genetics and vaccinology) whom I asked to comment on your as well as Ulrike Kämmerer et al. work, decided not to commentat all.
Keep up your excellent analysis!
Just so you know, in mental health SRA = Satanic Ritual Abuse.
That's exactly what I was thinking when I was first trying to figure out how to download gzipped reads fast from SRA. (The answer is to use parallel-fastq-dump or ENA, because fastq-dump is slow and fasterq-dump doesn't support gzip.)
When I'm doing these tutorials, I tell people to download reads from ENA instead which doesn't require installing any additional utilities:
curl 'https://www.ebi.ac.uk/ena/portal/api/filereport?accession=SRR18534011&result=read_run&fields=fastq_ftp'|sed 1d|cut -f2|tr \; \\n|sed s,^,ftp://,|xargs wget
This was way over my pay grade although I have a profound respect for the work and analysis done here. I’m going to re-read.
Oh my gosh - so much work (and hours) in this ‘solid resource with IT instructions’ article!! Thank you. Not only is this Substack post like a peer review (by renown Kevin McKernan) of a non peer-reviewed (but worthy of recognition) report (by Sandeep Chakraborty), but it’s affirmation of Sandeep’s collated written work - which by the way needs a date (2024) shown on page 1 or 13 on his report.
All this combined global work just helps towards the growing list from genome, virology and other experts, confirming high levels of DNA contamination being found in these novel but ‘bad’ and harmful C-19 jabs/shots.
P.S. This X post by ‘Fredy13’ on 11.12.2024 gives a Google doc of the list of “All current contamination papers linked”
McKernan
Nitta
Buckhaults
Koenig
Kirchner
Speicher
Raoult
Kaemmererlink
https://x.com/Fredy13_Backup/status/1866752447110320651
I think I would rather trust you, as I have all along to keep me attuned to what is going on, above my pay grade too Jesica!
Kevin emits sincerity. Don’t know him but totally trust him. He can even admit mistakes! What a novel idea.
I'm confused. After the first step, I have two fastq files, SRR18534011_1.fastq and SRR18534011_2.fastq.
They have lists of 120bp snippets, numbered identically in each file, but with entirely different bases. Eyeballing them, I'm pretty sure they're not the reverse reads of each other. What gives?
The start of my project (decided to go with a repo rather than a gist) is https://github.com/jcomeauictx/sudoku-verify/. Thanks!
jcomeau@LAPTOP-G5G3JKFM:/usr/src/jcomeauictx/sudoku-verify$ head -n 4 *.fastq
==> SRR18534011_1.fastq <==
@SRR18534011.1 R100400180029:V350023384:V350023384:1:135:1:4:CTTTGATG length=120
TAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGGATCGCTTGAGCCCAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAGTTCGGCATCAATATGGTGACCTCC
+SRR18534011.1 R100400180029:V350023384:V350023384:1:135:1:4:CTTTGATG length=120
FGFFFFFGEFGFBGFFDEBFFFGFFFFFFEFFFFFDFFFFFGFFFFFFFFFFEFGEFFFFFFFGFEFDFAG=GGFFF6EFGEFFF@FFFFFFFFEFEGFFFFFFDEDDGAD@E>FDDFGF
==> SRR18534011_2.fastq <==
@SRR18534011.1 R100400180029:V350023384:V350023384:1:135:1:4:CTTTGATG length=120
TGGTCCCCCGCTCCCGGGAGGTCACCATATTGATGCCGAACTTAGTGCGGACACCCGATCGGCATAGCGCACTACAGCCCAGAACTCCTGGGCTCAAGCGCTCCTCCCACCTCAGCCTCC
+SRR18534011.1 R100400180029:V350023384:V350023384:1:135:1:4:CTTTGATG length=120
DFFF>FGFGGFFGEFGGF@FFCFFGFGGGGGE?FGEEFFD7BEFGGF6DFFA;GFGFAFFE@BF6F<0FF?F;F8CFFG;GEF6DFGFGDFF09FGEEB6*FFGBFFFEFF8F8FFCFGE
jcomeau@LAPTOP-G5G3JKFM:/usr/src/jcomeauictx/sudoku-verify$
Glad you’re playing with this.
That’s totally normal.
The forward and reverse reads ideally never overlap but often do.
The DNBSEQ G400 has a unique nano ball library prep where DNA is circularized so the reads you get are from opposite sides of a 200-400bp molecule.
ChatGPT is aware of this and even has some descriptions of how their read orientations differ from Illuminas.
Samtools -F and -f functions I think are confused by it and I’m updating the stranded analysis this weekend.
Thank you for this review, which I can almost understand. My computing abilities are not at a sufficient level to use your tutorial.
I do have a question, however. There are two types of Pfizer (and Moderna) mRNA vaxxes- the original PCR-produced trial shots, and the plasmid public injections. Has anyone been able to obtain or assess the original shots, or samples from the trial subjects, in order to analyse the residual modRNA and cDNA?
I wonder how many people in the world have the expertise to navigate let alone duplicate Kevin’s work? It’s apparent that regulators wouldn’t have this depth of special knowledge. It is obvious that Kevin has the stick-to-itiveness, the sign of a very curious and intelligent mind. Thank you.
Why go to all that trouble when one can design a vaccine spike bait (or vector or SV40bait) to enrich? I don’t understand
Thats what we use. IDT lockdown probes that tile the whole plasmid. But we lose quantitive reads/million with this. RNA is a different beast. Lots of high copy transcripts you want to deplete. Just have to be careful when you do it.
For qualifying I would rather have QPCR. Maybe I am old school, but RNAseq is harder to quantify and it depends what you believe rather what it actually is.
No one wants to hear it, but for what it's worth...I believe in Jesus Christ's eminent return, to straighten back out the system of life He created so perfectly. By tampering, we can only do it harm. Does anyone believe that in heaven, tampering will be encouraged or needed?
Everything the "system" seeks after to enrich itself, is based on false science, which essentially are lies that obscure the truth. VERY few success stories can be told in this plethora of endeavors supposedly the "answer" to problematic issues.
I might change my view, if there EVER is shown to be REAL improvements made.
Just a quick ramble.
Ray
I'm confused, the paper isn't tracking mRNA from BNT162b2? It's looking at immune responses via RNA? I don't understand why this study is looked at in this context....?