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Recent Replies
Comment: MD5 Mismatch on chrY When Extracting CRAM Region Despite Correct Reference Genom
by
Pierre Lindenbaum
165k
> samtools faidx GRCh38_full_analysis_set_plus_decoy_hla.fa chrY | md5sum
AGAIN:
the checksum cannot be calculated from the raw output o…
Answer: Salmon RNA-Seq transcript quantification
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dsull
★
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I'm assuming "for windows" means you're trying to install it on Windows?
According to https://salmon.readthedocs.io/en/latest/building.htm…
Answer: Discrepancy in GEO2R vs. Raw Data Analysis: Significance of DEGs
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ATpoint
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GEO2R is very primitive. I would always download raw data and process myself. That is more reproducible. Then results are what they are, gi…
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ATpoint
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Usually, you perform some exploration like PCA and plotting metrics like sample2sample correlation, sequencing depth etc. to see whether a …
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
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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
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If I recall a prior discussion right, `samtools ` should download the correct reference from Ensembl per one of the `samtools` dev/maintain…
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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
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> => 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…
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