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Recent Replies
Comment: Error 134 while aligning using hisat2
by
Fabio Marroni
★
2.9k
Other instances of the same error were indeed related to disk [space][1]. Can you post the output of the command: `df -h /bams/`? Another p…
Comment: **Error: unable to open file or unable to determine types for file**
by
Pierre Lindenbaum
152k
```
Please ensure that your file is TAB delimited (e.g., cat -t FILE).
- Also ensure that your file has integer chromosome coordinates in t…
Comment: bgzip error 4
by
Pierre Lindenbaum
152k
I/O error. Where are you writing , which filesytem ? do you have enough space ? what is the output of
gzip < chr1.vcf.gz > chr1.vcf.gz…
Answer: Error: unable to open file or unable to determine types for file bed file
by
Neel
▴
10
**Error: unable to open file or unable to determine types for file**
Hi i am trying to run this commands **bedtools intersect -a Ec_k1…
Answer: Anti-miRNA oligonuclotide identification
by
Asan Emirsale
•
0
You should find complementary sequences to make the miRNA silent. Should it be the Biopython or another tool. The solution might be as simp…
Comment: counting reads in a fastq file using a refrence fasta file
by
vaslanzadeh
▴
10
Thanks, this works but it is extremely slow, is there any other alternatives?
Answer: HISAT2 output direct to bam sorted
by
ATpoint
68k
hisat2 --dta -x genome -1 ../fastq_zea_mays/SRR214880_1.fastq -2 ../fastq_zea_mays/SRR214880_2.fastq \
| samtools sort -o sorted.b…
Comment: Error: Please supply a reference FASTA/GBK/EMBL file with --reference
by
Neel
▴
10
Yeah, its working now thank you so much for your reply.
Comment: pooled-heterozygosity calculation
by
mmcui0018
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0
Hi, I'm having the exactly same issue here. I want to calculate the pooled *He* using Rubin's method. I have tried to find the script how t…
Comment: best way to learn bash scripting
by
Jeremy
▴
740
There's a good tutorial for beginners here:
[UNIX/Linux Tutorial for Beginners][1]
[1]: http://www.ee.surrey.ac.uk/Teaching/Unix/
Comment: difference between target sequencing technologies
by
GenoMax
125k
> Are there any limitations with hybridization capture technology?
Yes you should be able to capture any region subject to proper probe de…
Answer: Hugely different results between edgeR and DESeq2
by
Gordon Smyth
★
5.4k
DESeq2 is broadly analogous to edgeR's glm pipeline using glmLRT, which constructs genewise tests treating the estimated dispersions as kno…
Comment: Help converting .CYCHP to .txt or .csv or .vcf
by
Pierre Lindenbaum
152k
https://www.thermofisher.com/fr/fr/home/life-science/microarray-analysis/microarray-analysis-partners-programs/affymetrix-developers-networ…
Comment: Help converting .CYCHP to .txt or .csv
by
Sarah
•
0
Unfortunately I dont have the powertools program mentioned in the link
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