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这是2016年发表的文章中（A reference gene catalogue of the pig gut microbiome）的数据，从他们提供的数据链接里下载的。 周云燕 ***@***.*** ------------------ 原始邮件 ------------------ 发件人: "zhouyunyan/PIGC" ***@***.***>; 发送时间: 2023年11月18日(星期六) 晚上11:02 ***@***.***>; ***@***.***>; 主题: [zhouyunyan/PIGC] 03_Gene_Catalog有点问题需要咨询 (Issue #7) 老师您好 我在03_Gene_Catalog部分代码中有点问题需要咨询您。 cd ../../PGC bash ${Scripts}/BGI287_gene_info_deal.sh...
你好！ 是R1和R2，代码后期整理的，可能从R1复制过来忘记改了。谢谢指正！ 周云燕 ***@***.*** ------------------ 原始邮件 ------------------ 发件人: "zhouyunyan/PIGC" ***@***.***>; 发送时间: 2024年10月16日(星期三) 晚上10:43 ***@***.***>; ***@***.***>; 主题: [zhouyunyan/PIGC] 06_Abundance.sh问题请教 (Issue #8) 周老师您好，我在运行06_Abundance.sh时遇到一些问题，bwa mem -M -Y -t 8 -o sam/${SampleID}.sam ${GeneCatalog}/02_cdhit_cluster/PIGC90_cds.fna ${CleanData}/${SampleID}.clean_R1.fastq.gz ${CleanData}/${SampleID}.clean_R1.fastq.gz，这是bwa比对的代码，为什么两个序列用的都是${SampleID}.clean_R1.fastq.gz呢？ 期待您的答复，谢谢！ —...
I also found that the annotation database of kobas is not available when installing on a new server. I don't know where to download it now，so I copied the previously downloaded...
The .SAF file was generated based on the output from prodigal using a additional script. The SAF file has fixed formats, including "GeneID", "Chr", '"Start", “End”，“Strand”. ------------------ 原始邮件 ------------------ 发件人: "zhouyunyan/PIGC" ***@***.***>; 发送时间: 2022年6月18日(星期六) 上午10:45 ***@***.***>;...
Sorry, I didn't save the script generated .SAF and can't find it now. The messages were sent through QQ mailbox, maybe the "nbsp" is an incompatibility problem that leads to garbled...
Featurecount seems to only support GTF/SAF files, maybe you can try to convert gff to gtf format.
I think it is more convenient to extract the information from the FASTA file (nucleotide or protein sequence) generated by Prodigal to obtain the .SAF file. All needed information including...
I have graduated and did not keep the data and codes for this article. If you can provide a test file, I can try to re-write a script when I...
Using the following code, you can try. `grep "^>" test.protein.fa |awk -v FS="[>#]" -v OFS="\t" '{print $2,$3,$4,$5}' >test.out.txt`
A .SAF file needs "GeneID", "Chr", '"Start", “End”，“Strand”. The “test.out.txt” is not a .SAF file，you need to make .SAF file based on the information extracted from "test.protein.fa" by the code...