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有人转换过sra到bam文件吗?
avatar
j*p
2
sra 可以换bam吗?我只知道sra to fastq
avatar
l*1
3
同意楼下的
Step one
SRAto fastq
btw LZ be careful:
cited:
The problem you are experiencing is that the version of the SRA toolkit is
out of date and that there is now an un(der)documented option in fastq-dump
to dump paired end data from an SRA-lite submission. The guidance notes on
the NCBI website you refer to are for version 2.0.1, and state that they are
not up to date:
link:
//www.biostars.org/post/show/11111/how-to-convert-sra-lite-paired-end-
submission-to-fastq/
then try
FASTQ to BAM (version 1.56.0)
by tool:
httpS//test.g2.bx.psu.edu/root?tool_id=picard_FastqToSam
avatar
n*7
4
fastq怎么可以到bam呢?
需要align啊
或者直接转成unaligned的?这个不是多此一举吗

dump
are

【在 l**********1 的大作中提到】
: 同意楼下的
: Step one
: SRAto fastq
: btw LZ be careful:
: cited:
: The problem you are experiencing is that the version of the SRA toolkit is
: out of date and that there is now an un(der)documented option in fastq-dump
: to dump paired end data from an SRA-lite submission. The guidance notes on
: the NCBI website you refer to are for version 2.0.1, and state that they are
: not up to date:

avatar
w*w
5
新的sra toolkit里已经有一个sam-dump工具,跑10G以下的小文件没什么问题,100G以
上的,跑一个2,3个礼拜还可以接受。同时跑两个,performance马上不行,要20,30
个礼拜才能完成。
avatar
w*w
6
傻了,sam-dump可以直接extract。我们感兴趣的只有几个小region,抓出来很快。不幸
的是好几个大文件都出错了。
avatar
j*p
7
still did not get LZ's point. but whatever.
avatar
l*1
8
最新 plus 正版吗 那个soft?
Sam≂BAM format
pls refer:
What 'Picard' does?
FastqToSam converts FASTQ files to unaligned BAM files.
httPS://test.g2.bx.psu.edu/root?tool_id=picard_FastqToSam

【在 w****w 的大作中提到】
: 傻了,sam-dump可以直接extract。我们感兴趣的只有几个小region,抓出来很快。不幸
: 的是好几个大文件都出错了。

avatar
s*s
9
I think you mean cSRA to BAM? SRA to BAM 没有意义啊
avatar
w*w
10
我拿到的文件应该都是cSRA,虽然都是sra extension.

【在 s******s 的大作中提到】
: I think you mean cSRA to BAM? SRA to BAM 没有意义啊
avatar
w*w
11
原来以为只能用samtools从bam文件抽取区域,得把整个cSRA先转成bam,计算量会太大
。后来发现sam-dump有--aligned-region option,问题就解决了。

【在 j*p 的大作中提到】
: still did not get LZ's point. but whatever.
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