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Recent Replies
Comment: MD5 Mismatch on chrY When Extracting CRAM Region Despite Correct Reference Genom
by
GenoMax
149k
Do you need the original reads to map to the T2T genome or are you interested in the original reference to map to T2T genome. You do not ne…
Comment: MD5 Mismatch on chrY When Extracting CRAM Region Despite Correct Reference Genom
by
offset
•
0
>That means samtools is able to find the correct reference but the one you are downloading manually is incorrect.
The reference genomes G…
Comment: MD5 Mismatch on chrY When Extracting CRAM Region Despite Correct Reference Genom
by
GenoMax
149k
That means `samtools` is able to find the correct reference but the one you are downloading manually is incorrect.
> I need to get origi…
Comment: MD5 Mismatch on chrY When Extracting CRAM Region Despite Correct Reference Genom
by
offset
•
0
**no need to provide the -T option**
remove -T option I can get include chrY records. But not I want. I need to get original fasta file …
Comment: MD5 Mismatch on chrY When Extracting CRAM Region Despite Correct Reference Genom
by
offset
•
0
samtools view -H HG00465/HG00465.final.cram | grep -F '@SQ' | grep chrY
output:
@SQ SN:chrY LN:57227415 M5:ce3e31103…
Comment: Alphafold in colab - homotrimer
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sjp24
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Thank you very much for replying. I did try this but I could only get it to work for one sequence, but that's OK, thanks again.
Comment: fastq direction
by
GenoMax
149k
You may want to do this --> https://www.biostars.org/p/179035/#179037
Comment: MD5 Mismatch on chrY When Extracting CRAM Region Despite Correct Reference Genom
by
GenoMax
149k
If I recall a prior discussion right, `samtools ` should download the correct reference from Ensembl per one of the `samtools` dev/maintain…
Answer: CNV detection
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cmdcolin
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VCF files, just plain SNP VCF files for example, can provide several "signals" of information for detecting CNVs including
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Comment: MD5 Mismatch on chrY When Extracting CRAM Region Despite Correct Reference Genom
by
Pierre Lindenbaum
165k
> => no output for above command
ah sorry it's @SQ not @SEQ
> this is type error
again, the checksum cannot be calculated from the ra…
Comment: MD5 Mismatch on chrY When Extracting CRAM Region Despite Correct Reference Genom
by
offset
•
0
samtools view -H HG00465.final.cram | grep -F '@SEQ' | grep chrY
=> no output for above command
samtools faidx GRCh38_full_analysis_se…
Comment: MD5 Mismatch on chrY When Extracting CRAM Region Despite Correct Reference Genom
by
Pierre Lindenbaum
165k
> chrY-specific MD5 mismatch: samtools faidx GRCh38_full_analysis_set_plus_decoy_hla-20190212.fa chrY | md5sum
this is not the chrY seque…
Comment: When is it valid to use differentially expressed genes as input in WGCNA?
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Andrew
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I'm a newbie commenting five years later. Guys with the same confusion can refer to this paper. "Improved biomarker discovery through a plo…
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Yugan Gogul Muthukumar
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Thanks for letting me know, I would use this approach. I'm learning Data science by myself, I don't have any peer it would be nice if you c…
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andrew
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Sometimes getting the required information is very difficult
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