bam-readcount step stuck

StickHu commented 1 year ago

Sorry to disturb you,but I was stuck in the bam-readcount step.

The code provided is that `and run bam-readcount:

while read line do mag=$line

echo $mag

cd SplitBam
cd ${mag}

cp ../../Split/${mag}/${mag}_contigs.tsv ${mag}_contigs.tsv
samtools faidx ../../Split/${mag}/${mag}.fa

echo "${mag}_contigs.tsv"
mkdir ReadcountFilter
for bamfile in *_Filter.bam
do
    stub=${bamfile%_Filter.bam}`

Is ${mag}_contig.tsv the same as ${Cluster_1}/Cluster1_contig.tsv? I will appreciate it if you can reply as soon as possible.

StickHu commented 1 year ago

And if I have several samples, i can't figure out what can do to make the protocol done. Can you help me about that?

StickHu commented 1 year ago

Besides, I can't download all the data provided,such as the test data or the simulated reads

chrisquince / DESMAN

bam-readcount step stuck #52